,Location of variant,,,Alleles present within patient isolates,,,,CDS and gene product,,,,,Position on phylogenetic tree,,,,Variant type and length,,Ancestral allele typing,,,,
Patient,Variant name,Position in MRSA252,Position (reference),Allele 1,Allele 2,Codon 1,Codon 2,Effect on transcription,Protein effect,LocusID,MRSA252 ortholog,Product,Within carriage,Within disease,Between carriage/disease,Category,Variant type,Indel length,Ancestral allele in ML tree,Nasal isolate shares allele with MRCA in tree,Neighest neighbour allele on de novo assembly,carriage allele = neighbour allele,Concensus: ancestral or neighbour allele found in carriage population
P001,245239,245239,,C,T,CCA,TCA,Non-synonymous,Altering,SAR0211,SAR0211,conserved hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P001,1092247,1092247,,T,A,TTG,ATG,Non-synonymous,Altering,SAR1046,SAR1046,putative phosphoribosylglycinamide formyltransferase,1,0,0,C,SNP,0,T,1,T,1,1
P001,1161482,1161482,,A,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P001,1272466,1272466,,G,A,AGA,AAA,Non-synonymous,Altering,SAR1220,SAR1220,putative ribonuclease HII,1,0,0,C,SNP,0,G,1,G,1,1
P001,1275004,1275004,,C,T,CCT,CTT,Non-synonymous,Altering,SAR1222,SAR1222,putative succinyl-CoA ligase,1,0,0,C,SNP,0,C,1,C,1,1
P001,1392933,1392933,,A,C,ATT,ATG,Non-synonymous,Altering,SAR1343,SAR1343,amino acid permease,1,0,0,C,SNP,0,A,1,A,1,1
P001,1955663,1955663,,A,G,TTC,TCC,Non-synonymous,Altering,SAR1868,SAR1868,aldo/keto reductase family protein,1,0,0,C,SNP,0,A,1,A,1,1
P001,2251488,2251488,,G,A,GCA,GTA,Non-synonymous,Altering,SAR2180,SAR2180,putative thiamine-phosphate pyrophosphorylase,1,0,0,C,SNP,0,G,1,G,1,1
P001,2428365,2428365,,G,A,CCT,TCT,Non-synonymous,Altering,SAR2357,SAR2357,putative molybdenum cofactor biosynthesis protein,1,0,0,C,SNP,0,G,1,G,1,1
P001,2622238,2622238,,C,T,ACC,ATC,Non-synonymous,Altering,SAR2541,SAR2541,putative carboxylesterase,1,0,0,C,SNP,0,C,1,C,1,1
P001,2627065,2627065,,G,A,CAT,TAT,Non-synonymous,Altering,SAR2545,SAR2545,conserved hypothetical protein,1,0,0,C,SNP,0,G,1,G,1,1
P001,2786928,2786928,,A,G,GTT,GCT,Non-synonymous,Altering,SAR2696,SAR2696,putative transporter protein,1,0,0,C,SNP,0,A,1,A,1,1
P001,2823779,2823779,,A,C,AAT,CAT,Non-synonymous,Altering,SAR2723,SAR2723,putative exported protein,1,0,0,C,SNP,0,A,1,A,1,1
P001,k31_var_131,2884841,,G,GT,TTA,TTT,"Frameshift, stop gained",Truncating,SAR2778,SAR2778,nickel transporter NixA,1,0,0,C,ShINDEL,1,NA,NA,GT,1,1
P001,k31_var_138,NA,"318513(MSSA476, BX571857.1)",A,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,C,1,1
P001,k31_var_144,896083,,GA,G,AAG,AGA,"Frameshift, stop gained",Truncating,SAR0847,SAR0847,thermonuclease,1,0,0,C,ShINDEL,1,NA,NA,GA,1,1
P001,k31_var_149,NA,"2073296(MSSA476, BX571857.1)",TT,T,AGG,AGT,"Frameshift, stop gained",Truncating,SAS1927,(no ortholog),hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,TT,1,1
P001,k31_var_30,2024444,,T,TT,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,T,1,1
P002,k31_var_5063,NA,"1341628(MSSA476, BX571857.1)",C,T,CAA,TAA,Nonsense,Truncating,SAS1247,SAR1311,hypothetical protein,0,0,1,B,SNP,0,NA,NA,C,0,0
P003,1242271,1242271,,G,A,TTG,TTA,Synonymous,Silent,SAR1193,SAR1193,hypothetical protein,1,0,0,C,SNP,0,G,1,G,1,1
P003,1722912,1722912,,G,A,CAT,TAT,Non-synonymous,Altering,SAR1655,SAR1655,putative methyltransferase,1,0,0,C,SNP,0,G,1,G,1,1
P003,2595980,2595980,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P003,k31_var_65,722633,,T,TAAT,GCA,GAT,"Non-synonymous, 1 codon insertion",Altering,SAR0675,SAR0675,peptidase M23,1,0,0,C,ShINDEL,3,NA,NA,T,1,1
P004,381320,381320,,G,A,GGT,GAT,Non-synonymous,Altering,SAR0335,SAR0335,putative luciferase-like monooxygenase,0,0,1,B,SNP,0,G,1,G,1,1
P004,1968219,1968219,,A,T,GAT,GTT,Non-synonymous,Altering,SAR1881,SAR1881,putative lipoprotein,0,0,1,B,SNP,0,A,1,A,1,1
P004,2212970,2212970,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,1,G,1,1
P004,2595982,2595982,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,T,1,1
P004,2749530,2749530,,A,G,TTG,CTG,Synonymous,Silent,SAR2662,SAR2662,cobalamin synthesis protein/P47K family protein,0,0,1,B,SNP,0,A,1,A,1,1
P005,2540898,2540898,,G,C,GCC,CCC,Non-synonymous,Altering,SAR2468,SAR2468,AraC family regulatory protein,0,0,1,B,SNP,0,G,1,G,1,1
P005,k31_var_135,1027708,,AA,A,AGT,GTG,"Frameshift, stop gained",Truncating,SAR0982,SAR0982,hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,AA,1,1
P006,1552808,1552808,,G,C,GGT,GCT,Non-synonymous,Altering,SAR1461,SAR1461,penicillin-binding protein 2,1,0,0,C,SNP,0,G,1,G,1,1
P006,2578821,2578821,,T,C,GAA,GGA,Non-synonymous,Altering,SAR2506,SAR2506,putative phosphoglycerate mutase,1,0,0,C,SNP,0,T,1,T,1,1
P006,k31_var_9170,597889,,TACT,T,TTA,TTT,"Non-synonymous, 1 codon deletion",Altering,rpoC,SAR0548,DNA-directed RNA polymerase beta' chain protein,1,0,0,C,ShINDEL,3,NA,NA,TACT,1,1
P007,828951,828951,,C,T,ACA,ATA,Non-synonymous,Altering,SAR0790,SAR0790,lipoprotein,0,0,1,B,SNP,0,C,1,C,1,1
P007,1041867,1041867,,A,G,CAT,CGT,Non-synonymous,Altering,SAR0994,SAR0994,putative 5'-nucleotidase,1,0,0,C,SNP,0,A,1,A,1,1
P007,1784695,1784695,,A,G,ATT,ACT,Non-synonymous,Altering,SAR1719,SAR1719,queuine tRNA-ribosyltransferase,0,0,1,B,SNP,0,A,1,A,1,1
P007,1963446,1963446,,G,C,TCA,TGA,Nonsense,Truncating,SAR1876,SAR1876,hypothetical protein,0,1,0,D,SNP,0,G,1,G,1,1
P007,k31_var_84,NA,unknown,TC,T,TCT,TTC,"Frameshift, stop gained",Truncating,unknown,(no ortholog),putative helicase,0,0,1,B,ShINDEL,1,NA,NA,TC,1,1
P008,960313,960313,,C,T,GTT,ATT,Non-synonymous,Altering,SAR0923,SAR0923,putative argininosuccinate synthase,0,1,0,D,SNP,0,C,NA,C,1,1
P008,1661424,1661424,,G,A,GCA,GTA,Non-synonymous,Altering,SAR1589,SAR1589,"6-phosphogluconate dehydrogenase, decarboxylating",1,0,0,C,SNP,0,G,1,G,1,1
P008,k61_var_5,1766217,,CT,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,CT,1,1
P009,16203,16203,,A,G,GGA,GGG,Synonymous,Silent,SAR0012,SAR0012,putative hydrolase,1,0,0,C,SNP,0,A,1,A,1,1
P009,126675,126675,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,1,G,1,1
P009,362073,362073,,A,G,GCA,GCG,Synonymous,Silent,SAR0317,SAR0317,lipase precursor,1,0,0,C,SNP,0,A,1,A,1,1
P009,452660,452660,,T,C,GTT,GCT,Non-synonymous,Altering,SAR0422,SAR0422,exotoxin,1,0,0,C,SNP,0,T,1,T,1,1
P009,935153,935153,,A,G,GAT,GGT,Non-synonymous,Altering,SAR0899,SAR0899,conserved hypothetical protein,1,0,0,C,SNP,0,A,1,A,1,1
P009,986003,986003,,G,A,CCG,CCA,Synonymous,Silent,SAR0942,SAR0942,putative membrane protein,0,0,1,B,SNP,0,T,1,G,1,1
P009,1193867,1193867,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P009,1387013,1387013,,C,T,GCG,ACG,Non-synonymous,Altering,SAR1337,SAR1337,putative aspartate kinase,0,0,1,B,SNP,0,C,1,C,1,1
P009,1400341,1400341,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P009,1410166,1410166,,T,A,ATT,TTT,Non-synonymous,Altering,SAR1360,SAR1360,large-conductance mechanosensitive channel,1,0,0,C,SNP,0,T,1,T,1,1
P009,1464914,1464914,,A,G,ACA,GCA,Non-synonymous,Altering,SAR1406,SAR1406,aspartate semialdehyde dehydrogenase,1,0,0,C,SNP,0,A,1,A,1,1
P009,1489802,1489802,,G,A,TCG,TTG,Non-synonymous,Altering,SAR1430,SAR1430,putative UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyr ophosphoryl-undecaprenol N-acetylglucosamine transferase,1,0,0,C,SNP,0,G,1,G,1,1
P009,1702392,1702392,,T,C,ATT,GTT,Non-synonymous,Altering,SAR1634,SAR1634,putative endonuclease,1,0,0,C,SNP,0,T,1,T,1,1
P009,1789110,1789110,,T,C,AAA,GAA,Non-synonymous,Altering,SAR1724,SAR1724,Spo0B-associated GTP-binding protein,1,0,0,C,SNP,0,T,1,T,1,1
P009,1808983,1808983,,A,G,TTT,CTT,Non-synonymous,Altering,SAR1745,SAR1745,putative membrane protein,1,0,0,C,SNP,0,A,1,A,1,1
P009,1827979,1827979,,G,A,GCA,GTA,Non-synonymous,Altering,SAR1764,SAR1764,chromosome replication initiation/membrane attachment protein,1,0,0,C,SNP,0,G,1,G,1,1
P009,1932295,1932295,,T,C,GAT,GGT,Non-synonymous,Altering,SAR1843,SAR1843,leucyl-tRNA synthetase,1,0,0,C,SNP,0,T,1,T,1,1
P009,2601385,2601385,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,1,G,1,1
P009,k31_var_10,NA,"1991662(Newman, AP009351.1)",T,C,ACT,GCT,Non-synonymous,Altering,NWMN_1778,(no ortholog), conserved hypothetical protein,1,0,0,C,SNP,0,NA,NA,NA,NA,NA
P009,k31_var_111,342860,,A,AAAT,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,3,NA,NA,A,1,1
P009,k31_var_26,NA,unknown,A,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,NA,NA,NA
P009,k31_var_6,634605,,A,AT,TTT,TTT,"Frameshift, stop gained",Truncating,SAR0580,SAR0580,putative AMP-binding enzyme,1,0,0,C,ShINDEL,1,NA,NA,A,1,1
P010,4270,4270,,A,G,GAT,GGT,Non-synonymous,Altering,SAR0004,SAR0004,DNA replication and repair protein RecF,1,0,0,C,SNP,0,A,1,A,1,1
P010,14583,14583,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,1,G,1,1
P010,128823,128823,,G,A,CTT,TTT,Non-synonymous,Altering,SAR0117,SAR0117,putative siderophore transport system permease,1,0,0,C,SNP,0,G,1,G,1,1
P010,134317,134317,,A,G,GTA,GTG,Synonymous,Silent,SAR0122,SAR0122,putative transport protein,1,0,0,C,SNP,0,A,1,A,1,1
P010,143399,143399,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P010,173471,173471,,C,T,CCG,TCG,Non-synonymous,Altering,SAR0155,SAR0155,capsular polysaccharide synthesis enzyme,0,1,0,D,SNP,0,C,1,C,1,1
P010,376547,376547,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P010,393556,393556,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P010,427310,427310,,A,T,ACA,TCA,Non-synonymous,Altering,SAR0390,SAR0390,putative lipoprotein,1,0,0,C,SNP,0,A,1,A,1,1
P010,432930,432930,,C,A,GTT,TTT,Non-synonymous,Altering,SAR0398,SAR0398,alkyl hydroperoxide reductase subunit F,0,0,1,B,SNP,0,C,1,C,1,1
P010,505392,505392,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P010,738018,738018,,G,A,GAT,AAT,Non-synonymous,Altering,SAR0692,SAR0692,arsenate reductase,1,0,0,C,SNP,0,G,1,G,1,1
P010,900785,900785,,A,G,CAT,CGT,Non-synonymous,Altering,SAR0856,SAR0856,phosphoglycerate mutase family protein,1,0,0,C,SNP,0,A,1,A,1,1
P010,961816,961816,,G,A,GAT,AAT,Non-synonymous,Altering,SAR0924,SAR0924,putative glucose-6-phosphate isomerase,1,0,0,C,SNP,0,G,1,NA,NA,1
P010,987998,987998,,A,G,ATG,GTG,Non-synonymous,Altering,SAR0944,SAR0944,putative exported protein,1,0,0,C,SNP,0,A,1,A,1,1
P010,1035557,1035557,,C,T,GCG,GTG,Non-synonymous,Altering,SAR0990,SAR0990,peptide chain release factor 3,1,0,0,C,SNP,0,C,1,C,1,1
P010,1205089,1205089,,G,T,GTT,TTT,Non-synonymous,Altering,SAR1160,SAR1160,putative cell division protein,1,0,0,C,SNP,0,G,1,G,1,1
P010,1233696,1233696,,C,T,GCG,GTG,Non-synonymous,Altering,SAR1186,SAR1186,conserved hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P010,1394620,1394620,,T,C,GAT,GAC,Synonymous,Silent,SAR1344,SAR1344,catalase,1,0,0,C,SNP,0,T,1,T,1,1
P010,1416185,1416185,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,NA,NA,1
P010,1472722,1472722,,C,T,CGC,CAC,Non-synonymous,Altering,SAR1414,SAR1414,"COL, NC_002951.2d shock protein",1,0,0,C,SNP,0,C,1,C,1,1
P010,1521062,1521062,,C,T,AGT,AAT,Non-synonymous,Altering,SAR1447,SAR1447,very large surface anchored protein,0,0,1,B,SNP,0,C,1,C,1,1
P010,1532952,1532952,,T,G,AGT,CGT,Non-synonymous,Altering,SAR1447,SAR1447,very large surface anchored protein,1,0,0,C,SNP,0,T,1,T,1,1
P010,1707676,1707676,,A,G,ATT,ATC,Synonymous,Silent,SAR1639,SAR1639,DNA primase,1,0,0,C,SNP,0,A,1,A,1,1
P010,1725231,1725231,,G,T,CCT,ACT,Non-synonymous,Altering,SAR1657,SAR1657,chaperone protein,1,0,0,C,SNP,0,G,1,NA,NA,1
P010,1792518,1792518,,C,T,GGC,GAC,Non-synonymous,Altering,SAR1729,SAR1729,putative rod shape-determining protein,1,0,0,C,SNP,0,C,1,C,1,1
P010,1888285,1888285,,A,G,ATT,ATC,Synonymous,Silent,SAR1810,SAR1810,formate--tetrahydrofolate ligase,1,0,0,C,SNP,0,A,1,A,1,1
P010,1974816,1974816,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P010,2014344,2014344,,G,A,ACG,ATG,Non-synonymous,Altering,SAR1934,SAR1934,putative membrane protein,1,0,0,C,SNP,0,G,1,G,1,1
P010,2073936,2073936,,T,G,TTT,GTT,Non-synonymous,Altering,SAR1985,SAR1985,DNA polymerase III subunit epsilon,1,0,0,C,SNP,0,T,1,T,1,1
P010,2248360,2248360,,C,T,CAT,TAT,Non-synonymous,Altering,SAR2177,SAR2177,putative cardiolipin synthetase,0,0,1,B,SNP,0,C,1,C,1,1
P010,2315848,2315848,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P010,2414778,2414778,,C,T,CCG,CCA,Synonymous,Silent,SAR2342,SAR2342,putative membrane protein,0,0,1,B,SNP,0,C,1,C,1,1
P010,2432435,2432435,,G,A,GCG,GTG,Non-synonymous,Altering,SAR2362,SAR2362,putative molybdenum transport system permease protein,1,0,0,C,SNP,0,G,1,G,1,1
P010,2517568,2517568,,T,G,ATT,AGT,Non-synonymous,Altering,SAR2448,SAR2448,sensor kinase protein,0,0,1,B,SNP,0,T,1,T,1,1
P010,2562829,2562829,,A,G,AGT,AGC,Synonymous,Silent,SAR2488,SAR2488,nitrite reductase NAD(P)H small subunit,0,0,1,B,SNP,0,A,1,A,1,1
P010,2673719,2673719,,A,G,TCT,CCT,Non-synonymous,Altering,SAR2589,SAR2589,putative transporter protein,1,0,0,C,SNP,0,A,1,A,1,1
P010,1598859(self),1623150,,T,G,GAG,GGG,Non-synonymous,Altering,SAR1532,SAR1532,hypothetical protein,1,0,0,C,SNP,0,NA,NA,T,1,1
P010,1609495(self),NA,"1586129(M1, NC_021059.1)",A,G,TAT,TGT,Non-synonymous,Altering,BN843_14890,SAR1985,DNA polymerase III subunit epsilon,1,0,0,C,SNP,0,NA,NA,NA,NA,NA
P010,592618(self),656764,,T,C,GGT,GGC,Synonymous,Silent,SAR0607,SAR0607,hypothetical protein,0,0,1,B,SNP,0,NA,NA,C,1,1
P010,978219(self),1082528,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,NA,NA,NA
P010,k31_var_30,2309200,,T,TCT,GAA,GAG,"Frameshift, stop gained",Truncating,SAR2241,SAR2241,ABC transporter ATP-binding protein,1,0,0,C,ShINDEL,2,NA,NA,TCT,1,1
P010,k31_var_35,901735,,T,TA,TAT,TAT,"Frameshift, stop gained",Truncating,SAR0858,SAR0858,hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,TA,1,1
P010,k31_var_41,2378102,,G,A,ACG,ACA,Synonymous,Silent,hysA2,SAR2292,hyaluronate lyase precursor 2,1,0,0,C,SNP,0,NA,NA,G,1,1
P010,k31_var_43,2042034,,AA,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,AA,1,1
P010,k31_var_46,NA,"62624(CN1, NC_022226.1)",A,AA,AAA,AAG,"Frameshift, stop gained",Truncating,SAKOR_00058,(no ortholog),hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,A,1,1
P010,k61_var_15,2469465,,T,TA,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,TA,1,1
P010,k61_var_28,NA,"341777(ST398, NC_017333.1)",A,AA,AAA,AAT,"Frameshift, stop gained",Truncating,SAPIG0305,(no ortholog),transposase,1,0,0,C,ShINDEL,1,NA,NA,AA,1,1
P010,k61_var_33,890685,,A,ACTCAGACAGTGACTCAGACTCAGACAGCGATTCAGATTCCGACAGTGACTCAGACTCGGATAGCGATTCAGATTCCGACAGTGACTCAGACTCAGACAGTGACTCAGATTCAGATAGCGACTCAGACTCAGACAGTGACTCAGATTCCGATAGCGATTCAGATTCCGACAGTGATTCCGACTCAGACAGTGACTCAGATTCAGATAGCGATTCAGATTCCGACAGTGATTCCGACTCAGACAGCGATTCAGAATCAGATAATGACTCAGACTCAGACAGCGATTCAGA,GAA,GGA,"Non-synonymous, 96 codon insertion",Altering,SAR0842,SAR0842,clumping factor A,1,0,0,C,ShINDEL,288,NA,NA,ACTCAGACAGTGACTCAGACTCAGACAGCGATTCAGATTCCGACAGTGACTCAGACTCGGATAGCGATTCAGATTCCGACAGTGACTCAGACTCAGACAGTGACTCAGATTCAGATAGCGACTCAGACTCAGACAGTGACTCAGATTCCGATAGCGATTCAGATTCCGACAGTGATTCCGACTCAGACAGTGACTCAGATTCAGATAGCGATTCAGATTCCGACAGTGATTCCGACTCAGACAGCGATTCAGAATCAGATAATGACTCAGACTCAGACAGCGATTCAGA,1,1
P010,k61_var_44,1707939,,TATAACCGCCATACTCATC,T,ATT,ATT,"Non-synonymous, 6 codon deletion",Altering,dnaG,SAR1639,DNA primase,1,0,0,C,ShINDEL,18,NA,NA,TATAACCGCCATACTCATC,1,1
P012,1639028,1639028,,G,A,TCT,TTT,Non-synonymous,Altering,SAR1563,SAR1563,hypothetical protein,0,1,0,D,SNP,0,G,1,NA,NA,1
P013,505100,505100,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,0,G,0,0
P014,116211,116211,,T,G,ATT,ATG,Non-synonymous,Altering,SAR0109,SAR0109,putative transporter protein,0,0,1,B,SNP,0,T,0,T,0,0
P014,543217,543217,,A,G,TTA,TTG,Synonymous,Silent,SAR0504,SAR0504,putative transcription-repair coupling factor,0,0,1,B,SNP,0,A,0,A,0,0
P014,1241870,1241870,,T,C,TCA,CCA,Non-synonymous,Altering,SAR1193,SAR1193,hypothetical protein,0,0,1,B,SNP,0,T,0,T,0,0
P014,1305557,1305557,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,T,1,1
P014,1703859,1703859,,A,T,TAC,AAC,Non-synonymous,Altering,SAR1635,SAR1635,putative helicase,0,0,1,B,SNP,0,A,0,A,0,0
P014,1810077,1810077,,T,C,AAT,GAT,Non-synonymous,Altering,SAR1747,SAR1747,"glutamate-1-semialdehyde 2,1-aminomutase",0,0,1,B,SNP,0,T,1,T,1,1
P014,2493612,2493612,,T,C,ACT,GCT,Non-synonymous,Altering,SAR2424,SAR2424,putative aldose 1-epimerase,1,0,0,C,SNP,0,T,1,T,1,1
P014,2582021,2582021,,T,C,AAT,AAC,Synonymous,Silent,SAR2508,SAR2508,IgG-binding protein,0,0,1,B,SNP,0,T,0,T,0,0
P014,2751945,2751945,,T,C,ACA,ACG,Synonymous,Silent,SAR2664,SAR2664,hypothetical protein,1,0,0,C,SNP,0,T,1,T,1,1
P014,2813438,2813438,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,0,G,0,0
P014,k31_var_100,1692516,,T,TT,GAA,GAA,"Frameshift, stop gained",Truncating,SAR1622,SAR1622,metallo-beta-lactamase superfamily protein,0,0,1,B,ShINDEL,1,NA,NA,T,1,1
P014,k31_var_150,349262,,AA,A,AGA,GAA,"Frameshift, stop gained",Truncating,SAR0306,SAR0306,peptide ABC transporter ATP-binding protein,0,1,0,D,ShINDEL,1,NA,NA,AA,1,1
P014,k31_var_54,NA,"838095(MSSA476, BX571857.1)",AA,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,AA,1,1
P014,k31_var_80,1044723,,CCTCGTTTAACATCAAACTTAATTTGTACAAATCCTTTTTCAAATTTTTCCTCGCGTTCAAAGTTATATTTAGGGTTTCTACCATAATTCCATTCCCAAGTTCTATATTTGTCGTTACTTAACTTTTCAATATTTTCCCAATCTTCATCCGTTAATTTATATTCTTCTACTTCAGTTTCTCCAAAGATAGTTTTCAAGATGATTTTTTTAAATTCTTCAATTTCTAAAGGGTCATTTAAAAATTCTTGAATGTTTGCTA,C,GGT,GGT,"Non-synonymous, 86 codon deletion",Altering,SAR0997,SAR0997,putative lipoate-protein ligase A,1,0,0,C,ShINDEL,258,NA,NA,CCTCGTTTAACATCAAACTTAATTTGTACAAATCCTTTTTCAAATTTTTCCTCGCGTTCAAAGTTATATTTAGGGTTTCTACCATAATTCCATTCCCAAGTTCTATATTTGTCGTTACTTAACTTTTCAATATTTTCCCAATCTTCATCCGTTAATTTATATTCTTCTACTTCAGTTTCTCCAAAGATAGTTTTCAAGATGATTTTTTTAAATTCTTCAATTTCTAAAGGGTCATTTAAAAATTCTTGAATGTTTGCTA,1,1
P014,k61_var_65,124358,,T,TGTTGTTGTCTTCTTTGCCAGGTTTGTTGCCGTCTTCTTTGCCAGGTTTGTTGCCGTCTTCTTTACCAGGTTT,AAG,AAA,"Non-synonymous, 24 codon insertion",Altering,SAR0114,SAR0114,immunoglobulin G binding protein A precursor,0,0,1,B,ShINDEL,72,NA,NA,TGTTGTTGTCTTCTTTGCCAGGTTTGTTGCCGTCTTCTTTGCCAGGTTTGTTGCCGTCTTCTTTACCAGGTTT,0,0
P015,1324673,1324673,,G,A,GCT,ACT,Non-synonymous,Altering,SAR1262,SAR1262,putative exported protein,1,0,0,C,SNP,0,G,1,G,1,1
P015,2166347,2166347,,C,A,GCG,GAG,Non-synonymous,Altering,SAR2102,SAR2102,hypothetical phage protein,1,0,0,C,SNP,0,C,1,NA,NA,1
P016,1068083,1068083,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P017,170554,170554,,T,A,ATT,AAT,Non-synonymous,Altering,SAR0153,SAR0153,capsular polysaccharide synthesis enzyme,0,1,0,D,SNP,0,T,1,T,1,1
P017,213207,213207,,G,C,CTA,GTA,Non-synonymous,Altering,SAR0187,SAR0187,putative branched-chain amino acid transport system carrier protein,0,0,1,B,SNP,0,G,0,G,0,0
P017,588797,588797,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,1,G,1,1
P017,1232297,1232297,,T,C,TTA,TTG,Synonymous,Silent,SAR1184,SAR1184,conserved hypothetical protein,0,0,1,B,SNP,0,T,1,T,1,1
P017,1453572,1453572,,G,A,GGT,AGT,Non-synonymous,Altering,SAR1397,SAR1397,putative peptidase,0,0,1,B,SNP,0,G,1,G,1,1
P017,1480590,1480590,,C,T,GGT,AGT,Non-synonymous,Altering,SAR1423,SAR1423,hypothetical protein,0,0,1,B,SNP,0,C,0,C,0,0
P017,1530021,1530021,,A,G,TTA,CTA,Synonymous,Silent,SAR1447,SAR1447,very large surface anchored protein,0,0,1,B,SNP,0,A,1,A,1,1
P017,1580459,1580459,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,0,T,0,0
P017,1673349,1673349,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,0,A,0,0
P017,2308517,2308517,,C,T,GAA,AAA,Non-synonymous,Altering,SAR2240,SAR2240,haloacid dehalogenase-like hydrolase,0,0,1,B,SNP,0,C,0,C,0,0
P017,2370544,2370544,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,1,C,1,1
P017,2407192,2407192,,C,T,GAA,AAA,Non-synonymous,Altering,SAR2335,SAR2335,50S ribosomal protein L3,0,0,1,B,SNP,0,C,0,C,0,0
P017,2496430,2496430,,C,T,GAT,AAT,Non-synonymous,Altering,SAR2427,SAR2427,ABC transporter ATP-binding protein,0,0,1,B,SNP,0,C,1,C,1,1
P017,2571220,2571220,,A,G,GTT,GTC,Synonymous,Silent,SAR2497,SAR2497,conserved hypothetical protein,0,0,1,B,SNP,0,A,0,A,0,0
P017,2575711,2575711,,A,G,TTA,TCA,Non-synonymous,Altering,SAR2503,SAR2503,transport system membrane protein,0,0,1,B,SNP,0,A,1,A,1,1
P017,2684206,2684206,,G,A,GGC,AGC,Non-synonymous,Altering,SAR2597,SAR2597,putative membrane protein,0,0,1,B,SNP,0,G,0,G,0,0
P017,k31_var_134,2034099,,CAAATCCTATCTTCCGCTCCATAATTTAATAATAATGCGGGAGTATTTCAACTCTTAGAATACATTCCTTCCTGGAATGAGGTATAGGTGT,C,NA,NA,"Non-synonymous, 30 codon deletion",Altering,SAR_RS10035,SARt027,tRNA-Gly,0,0,1,B,ShINDEL,90,NA,NA,CAAATCCTATCTTCCGCTCCATAATTTAATAATAATGCGGGAGTATTTCAACTCTTAGAATACATTCCTTCCTGGAATGAGGTATAGGTGT,1,1
P017,k31_var_143,444285,,ATGGCGGTATTAAATTCTCAGGAGATATCATTAAAGCATTAGCTGCTGG,A,GAT,GAT,"Non-synonymous, 16 codon deletion",Altering,SAR0408,SAR0408,inosine-5-monophosphate dehydrogenase,0,0,1,B,ShINDEL,48,NA,NA,ATGGCGGTATTAAATTCTCAGGAGATATCATTAAAGCATTAGCTGCTGG,1,1
P018,765779,765779,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,1,G,1,1
P018,1179054,1179054,,C,T,TGT,TAT,Non-synonymous,Altering,SAR1133,SAR1133,putative membrane protein,1,0,0,C,SNP,0,C,1,C,1,1
P018,1513287,1513287,,C,T,GCA,ACA,Non-synonymous,Altering,SAR1447,SAR1447,very large surface anchored protein,1,0,0,C,SNP,0,C,1,C,1,1
P018,2183013,2183013,,A,G,GTA,GTG,Synonymous,Silent,SAR2121,SAR2121,putative carbon-nitrogen hydrolase,1,0,0,C,SNP,0,A,1,A,1,1
P018,2477642,2477642,,T,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,T,1,T,1,1
P018,2757805,2757805,,T,C,GAA,GAG,Synonymous,Silent,SAR2671,SAR2671,conserved hypothetical protein,1,0,0,C,SNP,0,T,1,NA,NA,1
P019,574041,574041,,G,A,GTA,ATA,Non-synonymous,Altering,SAR0528,SAR0528,putative stress response-related Clp ATPase,1,0,0,C,SNP,0,G,1,NA,NA,1
P019,726122,726122,,C,T,GTC,GTT,Synonymous,Silent,SAR0677,SAR0677,AraC family regulatory protein (pseudogene),1,0,0,C,SNP,0,C,1,C,1,1
P019,940465,940465,,G,A,ACG,ACA,Synonymous,Silent,SAR0904,SAR0904,cytosol aminopeptidase family protein,1,0,0,C,SNP,0,G,1,G,1,1
P019,1506273,1506273,,G,A,CAA,TAA,Nonsense,Truncating,SAR1447,SAR1447,very large surface anchored protein,0,0,1,B,SNP,0,G,1,G,1,1
P019,1542058,1542058,,A,G,TAT,TAC,Synonymous,Silent,SAR1453,SAR1453,hypothetical protein,1,0,0,C,SNP,0,A,1,A,1,1
P019,1552111,1552111,,T,G,AGT,AGG,Non-synonymous,Altering,SAR1460,SAR1460,putative recombination protein U,0,0,1,B,SNP,0,T,1,T,1,1
P019,1682572,1682572,,G,A,GCA,GTA,Non-synonymous,Altering,SAR1610,SAR1610,lipoate-protein ligase A protein,1,0,0,C,SNP,0,G,1,G,1,1
P019,1937465,1937465,,C,T,TGG,TGA,Nonsense,Truncating,SAR1847,SAR1847,repressor of toxins,0,0,1,B,SNP,0,C,1,C,1,1
P019,2269363,2269363,,T,C,TCA,TCG,Synonymous,Silent,SAR2201,SAR2201,serine hydroxymethyltransferase,1,0,0,C,SNP,0,T,1,T,1,1
P019,2296262,2296262,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,1,NA,NA,1
P019,2346749,2346749,,T,G,ACA,CCA,Non-synonymous,Altering,SAR2265,SAR2265,putative membrane protein,0,0,1,B,SNP,0,T,1,T,1,1
P019,2475731,2475731,,A,G,AGA,GGA,Non-synonymous,Altering,SAR2407,SAR2407,hypothetical protein,0,0,1,B,SNP,0,A,1,A,1,1
P019,2584507,2584507,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P019,2700550,2700550,,C,T,GAT,AAT,Non-synonymous,Altering,SAR2616,SAR2616,conserved hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P019,2787544,2787544,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,1,C,1,1
P019,2810728,2810728,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P019,2824609,2824609,,C,T,AGC,AGT,Synonymous,Silent,SAR2723,SAR2723,putative exported protein,0,0,1,B,SNP,0,C,1,C,1,1
P019,2831381,2831381,,T,C,GAA,GAG,Synonymous,Silent,SAR2728,SAR2728,preprotein translocase SecA subunit-like protein,0,0,1,B,SNP,0,T,1,T,1,1
P019,2857386,2857386,,A,G,TCA,CCA,Non-synonymous,Altering,SAR2753,SAR2753,lipase precursor,0,0,1,B,SNP,0,A,1,NA,NA,1
P019,k31_var_19,30800,,G,GT,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,G,1,1
P019,k31_var_6,570254,,AA,A,AAA,AAG,Frameshift with readthrough,Altering,SAR0523,SAR0523,SNO glutamine amidotransferase family protein,0,0,1,B,ShINDEL,1,NA,NA,AA,1,1
P020,637311,637311,,G,A,CAT,TAT,Non-synonymous,Altering,SAR0584,SAR0584,hypothetical protein,0,1,0,D,SNP,0,G,1,G,1,1
P020,1314739,1314739,,G,C,GTT,CTT,Non-synonymous,Altering,SAR1252,SAR1252,cell division protein FtsK,0,1,0,D,SNP,0,G,1,G,1,1
P020,k31_var_21,2155561,,A,G,NA,NA,Intergenic,Intergenic,SAR2082,SAR2082,Pseudogene,0,1,0,D,SNP,0,NA,NA,T,1,1
P020,k31_var_32,2380294,,TA,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,ShINDEL,1,NA,NA,TA,1,1
P021,218561,218561,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P021,854286,854286,,T,C,ATA,ACA,Non-synonymous,Altering,SAR0813,SAR0813,excinuclease ABC subunit A,1,0,0,C,SNP,0,T,1,T,1,1
P021,859313,859313,,C,T,GAC,GAT,Synonymous,Silent,SAR0816,SAR0816,putative acetyltransferase,1,0,0,C,SNP,0,C,1,C,1,1
P021,1587405,1587405,,T,C,CAA,CGA,Non-synonymous,Altering,SAR1491,SAR1491,hypothetical protein,0,0,1,B,SNP,0,T,1,T,1,1
P021,1783085,1783085,,C,T,GGG,GGA,Synonymous,Silent,SAR1717,SAR1717,putative protein-export membrane protein,1,0,0,C,SNP,0,C,1,C,1,1
P021,2717556,2717556,,A,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,A,1,A,1,1
P021,98364(self),124912,,T,C,AAC,AGC,Non-synonymous,Altering,SAR0114,SAR0114,immunoglobulin G binding protein A precursor,1,0,0,C,SNP,0,NA,NA,NA,NA,NA
P021,k31_var_17,151152,,T,TT,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,TT,1,1
P021,k31_var_6,2547497,,T,TT,AAA,AAA,"Frameshift, stop gained",Truncating,SAR2473,SAR2473,putative exported protein,1,0,0,C,ShINDEL,1,NA,NA,TT,1,1
P021,k31_var_95,2009656,,T,TATTTC,GTA,GTA,"Frameshift, stop gained",Truncating,SAR1929,SAR1929,HIT-family protein,1,0,0,C,ShINDEL,5,NA,NA,T,1,1
P022,909979,909979,,T,C,GTA,GCA,Non-synonymous,Altering,SAR0871,SAR0871,ABC transporter permease protein,0,0,1,B,SNP,0,T,0,T,0,0
P022,1051059,1051059,,C,T,GCG,ACG,Non-synonymous,Altering,SAR1005,SAR1005,putative membrane protein,1,0,0,C,SNP,0,C,1,C,1,1
P022,1548113,1548113,,G,A,CGT,TGT,Non-synonymous,Altering,SAR1456,SAR1456,conserved hypothetical protein,0,0,1,B,SNP,0,G,0,G,0,0
P022,2035351,2035351,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,0,G,0,0
P022,2072652,2072652,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,1,C,1,1
P022,2373398,2373398,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,1,G,1,1
P022,2420897,2420897,,C,A,GCG,TCG,Non-synonymous,Altering,SAR2346,SAR2346,putative peptidoglycan pentaglycine interpeptide biosynthesis protein,0,0,1,B,SNP,0,C,1,C,1,1
P022,2739358,2739358,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,0,T,0,0
P022,2828941,2828941,,C,A,GTT,TTT,Non-synonymous,Altering,SAR2726,SAR2726,conserved hypothetical protein,0,0,1,B,SNP,0,C,0,C,0,0
P022,k31_var_107,2229657,,TT,T,AAG,AGC,"Frameshift, stop gained",Truncating,SAR2161,SAR2161,hypothetical protein,0,0,1,B,ShINDEL,1,NA,NA,TT,0,0
P023,372544,372544,,C,T,GTA,ATA,Non-synonymous,Altering,SAR0326,SAR0326,putative membrane protein,0,1,0,D,SNP,0,C,1,C,1,1
P023,1690568,1690568,,G,A,ACA,ATA,Non-synonymous,Altering,SAR1620,SAR1620,putative membrane protein,1,0,0,C,SNP,0,G,1,G,1,1
P023,1846538,1846538,,C,A,AGT,ATT,Non-synonymous,Altering,SAR1776,SAR1776,pyruvate kinase,0,0,1,B,SNP,0,C,1,C,1,1
P023,2473932,2473932,,A,T,AAT,AAA,Non-synonymous,Altering,SAR2404,SAR2404,haloacid dehalogenase-like hydrolase,0,1,0,D,SNP,0,A,1,A,1,1
P023,190457(self),294098,,A,G,GTA,GTG,Synonymous,Silent,SAR0253,SAR0253,ribitol-5-phosphate dehydrogenase,0,0,1,B,SNP,0,NA,NA,G,1,1
P024,453267,453267,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,0,T,0,0
P024,633582,633582,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,0,A,0,0
P024,639293,639293,,C,A,CAG,AAG,Non-synonymous,Altering,SAR0586,SAR0586,putative uracil-DNA glycosylase,0,0,1,B,SNP,0,C,1,C,1,1
P024,886198,886198,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,1,C,1,1
P024,898012,898012,,T,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,T,1,1
P024,1260738,1260738,,A,G,AGA,AGG,Synonymous,Silent,SAR1210,SAR1210,putative chromosome partition protein,0,0,1,B,SNP,0,A,0,A,0,0
P024,1275375,1275375,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P024,1955331,1955331,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,0,C,0,0
P024,2129238,2129238,,A,G,TAT,TAC,Synonymous,Silent,SAR2040,SAR2040,autolysin,0,0,1,B,SNP,0,A,0,A,0,0
P024,2212259,2212259,,G,A,GGT,AGT,Non-synonymous,Altering,SAR2148,SAR2148,L-threonine dehydratase biosynthetic IlvA,0,0,1,B,SNP,0,G,0,G,0,0
P024,2720626,2720626,,G,A,GAA,AAA,Non-synonymous,Altering,SAR2633,SAR2633,TetR family regulatory protein,0,0,1,B,SNP,0,G,0,G,0,0
P024,2788499,2788499,,G,T,ACA,AAA,Non-synonymous,Altering,SAR2697,SAR2697,conserved hypothetical protein,0,0,1,B,SNP,0,G,1,G,1,1
P024,k31_var_81,168617,,ATA,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,2,NA,NA,ATA,1,1
P024,k61_var_50,907411,,G,GACCACCCCAACTTGCATTGCTTGTAAGCTGACTTACCGTCAGCTTCTATGTTGGGG,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,56,NA,NA,GACCACCCCAACTTGCATTGCTTGTAAGCTGACTTACCGTCAGCTTCTATGTTGGGG,0,0
P025,285491,285491,,C,T,GGC,GGT,Synonymous,Silent,SAR0243,SAR0243,putative zinc-binding dehydrogenase,1,0,0,C,SNP,0,C,1,C,1,1
P025,307354,307354,,T,C,AAT,AAC,Synonymous,Silent,SAR0263,SAR0263,putative PTS transport system protein,1,0,0,C,SNP,0,T,1,T,1,1
P025,401339,401339,,C,T,TTG,TTA,Synonymous,Silent,SAR0354,SAR0354,conserved hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P025,498630,498630,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,G,1,G,1,1
P025,527962,527962,,C,T,GCG,GTG,Non-synonymous,Altering,SAR0490,SAR0490,tetrapyrrole (corrin/porphyrin) methylase family protein,1,0,0,C,SNP,0,C,1,C,1,1
P025,928804,928804,,A,G,AAA,GAA,Non-synonymous,Altering,SAR0892,SAR0892,D-isomer specific 2-hydroxyacid dehydrogenase,0,0,1,B,SNP,0,A,1,A,1,1
P025,1038552,1038552,,A,T,ACA,ACT,Synonymous,Silent,SAR0992,SAR0992,putative protease,0,1,0,D,SNP,0,A,1,A,1,1
P025,1091928,1091928,,A,G,GCA,GCG,Synonymous,Silent,SAR1046,SAR1046,putative phosphoribosylglycinamide formyltransferase,0,0,1,B,SNP,0,A,1,A,1,1
P025,1209425,1209425,,T,A,TAT,AAT,Non-synonymous,Altering,SAR1163,SAR1163,conserved hypothetical protein,0,0,1,B,SNP,0,T,1,T,1,1
P025,1336451,1336451,,G,A,GTG,GTA,Synonymous,Silent,SAR1272,SAR1272,DNA mismatch repair protein MutL,0,0,1,B,SNP,0,G,1,G,1,1
P025,1344926,1344926,,C,G,TTC,TTG,Non-synonymous,Altering,SAR1279,SAR1279,conserved hypothetical protein,0,0,1,B,SNP,0,C,1,C,1,1
P025,1504036,1504036,,C,T,AAG,AAA,Synonymous,Silent,SAR1447,SAR1447,very large surface anchored protein,0,0,1,B,SNP,0,C,1,C,1,1
P025,1581295,1581295,,T,G,GGA,GGC,Synonymous,Silent,SAR1486,SAR1486,cytidylate kinase,0,0,1,B,SNP,0,T,1,T,1,1
P025,1693738,1693738,,G,A,TCA,TTA,Non-synonymous,Altering,SAR1624,SAR1624,glucokinase,1,0,0,C,SNP,0,G,1,G,1,1
P025,1714408,1714408,,C,T,GGA,GAA,Non-synonymous,Altering,SAR1645,SAR1645,cytidine deaminase,0,1,0,D,SNP,0,C,1,C,1,1
P025,1872716,1872716,,C,T,TTG,TTA,Synonymous,Silent,SAR1798,SAR1798,conserved hypothetical protein,0,0,1,B,SNP,0,C,1,C,1,1
P025,2084674,2084674,,G,A,GTT,ATT,Non-synonymous,Altering,SAR1994,SAR1994,high affinity proline permease,1,0,0,C,SNP,0,G,1,G,1,1
P025,2328570,2328570,,G,A,GGC,GGT,Synonymous,Silent,SAR2252,SAR2252,putative phosphoglucosamine mutase,1,0,0,C,SNP,0,G,1,G,1,1
P025,2743111,2743111,,A,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,1,A,1,1
P025,2752462,2752462,,G,T,ACA,AAA,Non-synonymous,Altering,SAR2664,SAR2664,hypothetical protein,1,0,0,C,SNP,0,G,1,G,1,1
P025,2842102,2842102,,C,T,GGA,AGA,Non-synonymous,Altering,SAR2734,SAR2734,serine-rich adhesin for platelets,1,0,0,C,SNP,0,C,1,C,1,1
P025,2088061(self),NA,"1888223(MSSA476, BX571857.1)",G,A,GCA,GTA,Non-synonymous,Altering,SAS1739,(no ortholog),putative lantibiotic ABC transporter protein,0,1,0,D,SNP,0,NA,NA,G,1,1
P025,483864(self),289235,,A,G,AGG,AGA,Synonymous,Silent,SAR0248,SAR0248,hypothetical protein,1,0,0,C,SNP,0,NA,NA,A,1,1
P025,528922(self),NA,"317318(MSSA476, BX571857.1)",C,T,AGC,AGT,Synonymous,Silent,SAS0268,(no ortholog),hypothetical protein,0,1,0,D,SNP,0,NA,NA,C,1,1
P025,606786(self),428165,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,A,1,1
P025,k31_var_30,724883,,T,TA,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,1,NA,NA,T,1,1
P025,k31_var_61,886060,,TTAATTCTTCATT,T,GAC,GAA,Non-synonymous and 4 codon deletion,Altering,SAR0839,SAR0839,hypothetical protein,1,0,0,C,ShINDEL,12,NA,NA,TAATTCTTCATT,1,1
P025,k31_var_83,NA,"2662342(ED98, NC_013450.1)",AT,A,ATG,TGT,"Frameshift, stop gained",Truncating,SAAV_2632,SAR2648,secretory antigen precursor,1,0,0,C,ShINDEL,1,NA,NA,AT,1,1
P025,k31_var_94,NA,"893967(ED98, NC_013450.1)",T,C,AAA,GAA,Non-synonymous,Altering,SAAV_0876,(no ortholog),phage amidase,1,0,0,C,SNP,0,NA,NA,NA,NA,NA
P025,k61_var_29,890524,,TTCAGATAGTGACTCAGACTCAGACAGCGATTCAGAATCAGATAGTGACTCCGATTCAGACAGCGATTCAGAA,T,TCA,TCA,"Non-synonymous, 24 codon deletion",Altering,SAR0842,SAR0842,clumping factor A,1,0,0,C,ShINDEL,72,NA,NA,TTCAGATAGTGACTCAGACTCAGACAGCGATTCAGAATCAGATAGTGACTCCGATTCAGACAGCGATTCAGAA,1,1
P025,k61_var_34,NA,"907712(COL, NC_002951.2)",T,TT,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,NA,NA,NA
P026,731656,731656,,C,T,TCA,TTA,Non-synonymous,Altering,SAR0684,SAR0684,putative sugar efflux transporter,0,0,1,B,SNP,0,C,0,C,0,0
P026,1560459,1560459,,G,A,CCG,TCG,Non-synonymous,Altering,SAR1466,SAR1466,conserved hypothetical protein,0,0,1,B,SNP,0,G,1,G,1,1
P026,1580911,1580911,,A,C,ATT,ATG,Non-synonymous,Altering,SAR1486,SAR1486,cytidylate kinase,0,1,0,D,SNP,0,A,1,A,1,1
P026,1659300,1659300,,C,T,GGA,AGA,Non-synonymous,Altering,SAR1587,SAR1587,PfkB family carbohydrate kinase,0,0,1,B,SNP,0,C,1,C,1,1
P026,2270944,2270944,,G,A,GCG,GTG,Non-synonymous,Altering,SAR2204,SAR2204,conserved hypothetical protein,0,0,1,B,SNP,0,G,0,G,0,0
P026,k31_var_136,2172764,,A,AA,AAT,AAA,"Frameshift, stop gained",Truncating,SAR2109,SAR2109, succinyl-diaminopimelate desuccinylase,0,0,1,B,ShINDEL,1,NA,NA,AA,0,0
P026,k31_var_139,2157536,,T,TT,ACA,AAC,"Frameshift, stop gained",Truncating,SAR2085,SAR2085,"hypothetical protein, Similar to bacteriophage phi PVL ",0,0,1,B,ShINDEL,1,NA,NA,T,1,1
P027,377802,377802,,G,A,GGA,GAA,Non-synonymous,Altering,SAR0331,SAR0331,putative membrane protein,0,0,1,B,SNP,0,G,1,NA,NA,1
P027,511486,511486,,A,T,TTA,TTT,Non-synonymous,Altering,SAR0477,SAR0477,"DNA polymerase III, tau subunit",0,1,0,D,SNP,0,A,1,A,1,1
P027,681772,681772,,G,A,TTG,TTA,Synonymous,Silent,SAR0634,SAR0634,putative membrane protein,1,0,0,C,SNP,0,G,1,G,1,1
P027,2885303,2885303,,T,G,TGG,GGG,Non-synonymous,Altering,SAR2778,SAR2778,nickel transporter NixA,1,0,0,C,SNP,0,T,1,T,1,1
P027,k31_var_70,498622,,TA,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,T,0,0
P027,k31_var_77,472581,,TA,T,ATT,TTG,"Frameshift, stop gained",Truncating,SAR0445,SAR0445, hypothetical protein,0,0,1,B,ShINDEL,1,NA,NA,TA,1,1
P028,895560,895560,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,1,NA,NA,1
P028,k31_var_81,NA,"69483 (USA300_FPR3757, CP000255.1 )",C,T,GTT,TTT,Non-synonymous,Altering,arcC,SAR2711,carbamate kinase,0,0,1,B,SNP,0,NA,NA,C,1,1
P030,168668,168668,,T,C,ACA,ATA,Non-synonymous,Altering,SAR0151,SAR0151,capsular polysaccharide synthesis enzyme,1,0,0,C,SNP,0,C,1,C,1,1
P030,587072,587072,,A,G,AAA,AAG,Synonymous,Silent,SAR0540,SAR0540,transcription antitermination protein,1,0,0,C,SNP,0,G,1,G,1,1
P030,842363,842363,,A,G,ACA,GCA,Non-synonymous,Altering,SAR0804,SAR0804,putative helicase,1,0,0,C,SNP,0,A,1,A,1,1
P030,960522,960522,,T,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P030,1383481,1383481,,T,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P030,1827325,1827325,,G,A,GGC,GGT,Synonymous,Silent,SAR1763,SAR1763,putative primosomal protein,1,0,0,C,SNP,0,G,1,G,1,1
P030,1847196,1847196,,C,A,GGC,TGC,Non-synonymous,Altering,SAR1777,SAR1777,6-phosphofructokinase,1,0,0,C,SNP,0,C,1,NA,NA,1
P030,2063946,2063946,,A,G,ACA,ACG,Synonymous,Silent,SAR1973,SAR1973,putative membrane protein,1,0,0,C,SNP,0,A,1,A,1,1
P030,2229239,2229239,,T,C,GGA,GGG,Synonymous,Silent,SAR2161,SAR2161,putative membrane protein,1,0,0,C,SNP,0,T,1,T,1,1
P030,2322132,2322132,,G,T,GCT,GAT,Non-synonymous,Altering,SAR2248,SAR2248,putative surface anchored protein (pseudogene),1,0,0,C,SNP,0,G,1,G,1,1
P030,320888(self),341390,,A,T,ACT,ACA,Synonymous,Silent,SAR0297,SAR0297,conserved hypothetical protein (pseudogene),1,0,0,C,SNP,0,NA,NA,NA,NA,NA
P030,k31_var_24,NA,"642592(MSSA476, BX571857.1)",C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,C,1,1
P030,k31_var_28,NA,"1900559(MSSA476, BX571857.1)",A,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,C,1,1
P030,k31_var_32,450404,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,T,1,1
P030,k31_var_37,16075,,TT,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,TT,1,1
P030,k31_var_38,NA,"1556682(MSSA476, BX571857.1)",C,CT,AAA,AAG,"Frameshift, stop gained",Truncating,SAS1429,SAR1563,hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,C,1,1
P030,k31_var_8,1887181,,T,TT,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,TT,1,1
P030,k61_var_18,2460867,,A,AT,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,AT,1,1
P031,212538,212538,,C,T,GAT,AAT,Non-synonymous,Altering,SAR0187,SAR0187,putative branched-chain amino acid transport system carrier protein,1,0,0,C,SNP,0,C,1,C,1,1
P031,325462,325462,,T,G,TTT,TGT,Non-synonymous,Altering,SAR0280,SAR0280,putative membrane protein,0,0,1,B,SNP,0,T,1,T,1,1
P031,573557,573557,,G,A,GAA,AAA,Non-synonymous,Altering,SAR0527,SAR0527,putative phosphotransferase,1,0,0,C,SNP,0,G,1,G,1,1
P031,901128,901128,,C,T,GCG,ACG,Non-synonymous,Altering,SAR0857,SAR0857,putative LysE type translocator protein,1,0,0,C,SNP,0,C,1,C,1,1
P031,1278056,1278056,,C,A,GCA,GAA,Non-synonymous,Altering,SAR1225,SAR1225,SMF family protein,0,1,0,D,SNP,0,C,1,C,1,1
P031,1472409,1472409,,AA,TT,TTA,TAA,Nonsense,Truncating,SAR1413,SAR1413,putative membrane protein,0,0,1,B,SNP,0,NA,NA,AA,1,1
P031,1872900,1872900,,C,T,CGT,CAT,Non-synonymous,Altering,SAR1798,SAR1798,conserved hypothetical protein,0,0,1,B,SNP,0,C,1,C,1,1
P031,1887850,1887850,,T,C,TTA,TTG,Synonymous,Silent,SAR1810,SAR1810,formate--tetrahydrofolate ligase,0,0,1,B,SNP,0,T,1,T,0,0
P031,1964195,1964195,,T,C,ACA,GCA,Non-synonymous,Altering,SAR1877,SAR1877,AMP-binding enzyme,1,0,0,C,SNP,0,T,0,T,1,1
P031,2204354,2204354,,G,A,GGC,GAC,Non-synonymous,Altering,SAR2141,SAR2141,acetolactate synthase large subunit,1,0,0,C,SNP,0,G,1,G,1,1
P031,2383759,2383759,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P031,2420965,2420965,,A,G,GTA,GCA,Non-synonymous,Altering,SAR2346,SAR2346,putative peptidoglycan pentaglycine interpeptide biosynthesis protein,1,0,0,C,SNP,0,A,1,A,1,1
P031,2426400,2426400,,C,T,GTA,ATA,Non-synonymous,Altering,SAR2352,SAR2352,putative molybdenum cofactor biosynthesis protein A,1,0,0,C,SNP,0,C,1,C,1,1
P031,2500052,2500052,,C,A,GCA,GAA,Non-synonymous,Altering,SAR2430,SAR2430,putative permease,0,0,1,B,SNP,0,C,1,C,1,1
P031,2774589(self),NA,unknown,C,T,GGG,AGG,Non-synonymous,Altering,SAR0736,SAR0736,putative undecaprenol kinase,0,0,1,B,SNP,0,NA,NA,NA,NA,NA
P031,k31_var_108,907304,,CC,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,C,1,1
P031,k31_var_111,622996,,TT,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,TT,1,1
P031,k31_var_16,795756,,TCATGATATCAAGTAC,T,ATG,ATG,"Non-synonymous, 5 codon deletion",Altering,saeR,SAR0759,response regulator protein,0,0,1,B,ShINDEL,15,NA,NA,TCATGATATCAAGTAC,1,1
P031,k31_var_42,2186595,,T,TT,GAA,TGA,"Frameshift, stop gained",Truncating,agrA,SAR2126,autoinducer sensor protein response regulator protein,0,0,1,B,ShINDEL,1,NA,NA,T,1,1
P031,k31_var_45,NA,"3969(Strain 2395, NZ_CP007500.1)",AA,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,NA,NA,NA
P031,k31_var_56,667726,,T,TA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,T,1,1
P032,161796,161796,,A,G,GAA,GGA,Non-synonymous,Altering,SAR0147,SAR0147,putative nucleotidase,1,0,0,C,SNP,0,A,1,A,1,1
P032,187131,187131,,C,T,GCC,GCT,Synonymous,Silent,SAR0169,SAR0169,putative aldehyde dehydrogenase,1,0,0,C,SNP,0,C,1,C,1,1
P032,367259,367259,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P032,1116536,1116536,,C,T,AAC,AAT,Synonymous,Silent,SAR1070,SAR1070,dihydrolipoamide dehydrogenase,1,0,0,C,SNP,0,C,1,C,1,1
P032,1535328,1535328,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P032,2164296,2164296,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P032,2294348,2294348,,T,C,ATT,ATC,Synonymous,Silent,SAR2226,SAR2226,putative purine nucleoside phosphorylase,1,0,0,C,SNP,0,T,1,T,1,1
P032,2402654,2402654,,C,T,GAA,AAA,Non-synonymous,Altering,SAR2326,SAR2326,30S ribosomal protein S17,1,0,0,C,SNP,0,C,1,C,1,1
P032,2432568,2432568,,A,T,ATA,TTA,Non-synonymous,Altering,SAR2362,SAR2362,putative molybdenum transport system permease protein,0,0,1,B,SNP,0,T,1,T,1,1
P032,2810752,2810752,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P032,1725172(self),NA,"1899020(MSSA476, BX571857.1)",A,G,AAC,AAT,Synonymous,Silent,SAR2509,SAR2509,gamma-hemolysin component A precursor,1,0,0,C,SNP,0,NA,NA,A,1,1
P032,k31_var_102,1719358,,T,TT,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,TT,1,1
P032,k31_var_105,2524300,,A,AA,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,T,1,1
P032,k31_var_109,NA,"487795(ED98, NC_013450.1)",CAGCGATTCAGATTCGGAT,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,18,NA,NA,CAGCGATTCAGATTCGGAT,1,1
P032,k31_var_115,NA,"845157(N315, NC_002745.2)",GT,G,AAA,AAC,"Frameshift, stop gained",Truncating,SA0739,SAR0839,hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,GT,1,1
P032,k31_var_116,NA,"80194(ED98, NC_013450.1)",A,C,ATT,ATG,Non-synonymous,Altering,SAAV_0074,(no ortholog),integral membrane domain-containing protein,1,0,0,C,SNP,0,NA,NA,A,1,1
P032,k31_var_117,774790,,T,TT,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,TT,1,1
P032,k61_var_77,536006,,A,AGTTTTTTTAGTTTGTATTAAT,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,21,NA,NA,A,1,1
P033,1417010,1417010,,C,A,CGC,CTC,Non-synonymous,Altering,SAR1365,SAR1365,putative membrane protein,1,0,0,C,SNP,0,C,1,C,1,1
P033,1713488,1713488,,T,C,AAA,GAA,Non-synonymous,Altering,SAR1644,SAR1644,putative GTP-binding protein,0,1,0,D,SNP,0,T,1,T,1,1
P034,356539,356539,,C,T,GTG,GTA,Synonymous,Silent,SAR0312,SAR0312,putative N-acetylneuraminate lyase,0,0,1,B,SNP,0,C,1,C,1,1
P034,1160296,1160296,,G,A,GCC,GCT,Synonymous,Silent,SAR1113,SAR1113,putative ribonuclease,0,0,1,B,SNP,0,G,0,G,0,0
P034,1943879,1943879,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,0,G,0,0
P034,2106319,2106319,,C,T,TAC,TAT,Synonymous,Silent,SAR2013,SAR2013,putative aldehyde dehydrogenase,0,0,1,B,SNP,0,C,0,C,0,0
P034,2873122,2873122,,C,A,GGG,GGT,Synonymous,Silent,SAR2770,SAR2770,conserved hypothetical protein,1,0,0,C,SNP,0,A,1,A,1,1
P034,1364609(self),1554347,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,C,1,1
P034,k31_var_29,2608756,,GT,G,AAA,AAC,"Frameshift, stop gained",Truncating,SAR2530,SAR2530,putative membrane protein,0,0,1,B,ShINDEL,1,NA,NA,NA,NA,NA
P035,464354,464354,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,G,1,G,1,1
P035,502479,502479,,G,A,GGC,GAC,Non-synonymous,Altering,SAR0471,SAR0471,"glutamate synthase, large subunit",1,0,0,C,SNP,0,G,1,G,1,1
P035,590244,590244,,T,C,GCT,GCC,Synonymous,Silent,SAR0546,SAR0546,conserved hypothetical protein,1,0,0,C,SNP,0,T,1,T,1,1
P035,719006,719006,,A,G,AAC,AGC,Non-synonymous,Altering,SAR0672,SAR0672,putative ABC transporter permease,1,0,0,C,SNP,0,A,1,A,1,1
P035,1330420,1330420,,C,A,GGC,GGA,Synonymous,Silent,SAR1268,SAR1268,conserved hypothetical protein,0,1,0,D,SNP,0,C,1,C,1,1
P035,2103145,2103145,,C,T,GCA,ACA,Non-synonymous,Altering,SAR2010,SAR2010,hypothetical protein,0,1,0,D,SNP,0,C,1,C,1,1
P035,2630358,2630358,,T,C,AGT,AGC,Synonymous,Silent,SAR2548,SAR2548,putative membrane protein,1,0,0,C,SNP,0,T,1,T,1,1
P036,1560188,1560188,,T,C,GAT,GGT,Non-synonymous,Altering,SAR1466,SAR1466,conserved hypothetical protein,1,0,0,C,SNP,0,T,1,T,1,1
P037,197492,197492,,C,T,GCT,GTT,Non-synonymous,Altering,SAR0179,SAR0179,putative transporter protein,0,1,0,D,SNP,0,C,1,C,1,1
P037,357213,357213,,C,T,TCA,TTA,Non-synonymous,Altering,SAR0313,SAR0313,putative ROK family protein,1,0,0,C,SNP,0,C,1,C,1,1
P037,502814,502814,,G,A,GAT,AAT,Non-synonymous,Altering,SAR0471,SAR0471,"glutamate synthase, large subunit",1,0,0,C,SNP,0,G,1,G,1,1
P037,1017287,1017287,,A,T,GGA,GGT,Synonymous,Silent,SAR0974,SAR0974,conserved hypothetical protein,1,0,0,C,SNP,0,A,1,A,1,1
P037,1125989,1125989,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P037,1262226,1262226,,G,T,AAG,AAT,Non-synonymous,Altering,SAR1210,SAR1210,putative chromosome partition protein,1,0,0,C,SNP,0,G,1,G,1,1
P037,2044472,2044472,,T,A,TTA,ATA,Non-synonymous,Altering,SAR1954,SAR1954,"putative glutamate-1-semialdehyde 2,1-aminomutase",0,1,0,D,SNP,0,T,1,T,1,1
P037,2125575,2125575,,A,G,ATT,GTT,Non-synonymous,Altering,SAR2034,SAR2034,putative membrane protein,0,1,0,D,SNP,0,A,1,A,1,1
P037,1761181(self),NA,"1902152(MSSA476, BX571857.1)",A,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,T,1,1
P037,358352(self),470210,,T,A,ATG,AAG,Non-synonymous,Altering,SAR0442,SAR0442,hypothetical protein,1,0,0,C,SNP,0,NA,NA,T,1,1
P037,k31_var_51,2122235,,TA,A,AAT,AAA,"Frameshift, stop gained",Truncating,SAR2030,SAR2030,protein map (MHC analogous protein),1,0,0,C,ShINDEL,1,NA,NA,TA,1,1
P037,k61_var_81,NA,"604491(Newman, AP009351.1)",C,A,CGT,AGT,Non-synonymous,Altering,sdrC,SAR0566,serine-aspartate repeat-containing protein C,0,1,0,D,SNP,0,NA,NA,C,1,1
P038,227967,227967,,G,A,CCT,CTT,Non-synonymous,Altering,SAR0198,SAR0198,ABC transporter ATP-binding protein,0,0,1,B,SNP,0,G,1,G,1,1
P040,129955,129955,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,NA,NA,1
P040,173112,173112,,C,T,ACA,ATA,Non-synonymous,Altering,SAR0155,SAR0155,capsular polysaccharide synthesis enzyme,1,0,0,C,SNP,0,C,1,C,1,1
P040,182010,182010,,G,A,GTA,ATA,Non-synonymous,Altering,SAR0164,SAR0164,capsular polysaccharide synthesis enzyme,1,0,0,C,SNP,0,G,1,G,1,1
P040,207989,207989,,G,T,CCC,ACC,Non-synonymous,Altering,SAR0183,SAR0183,putative amino acid kinase,1,0,0,C,SNP,0,G,1,NA,NA,1
P040,358134,358134,,C,T,AGC,AAC,Non-synonymous,Altering,SAR0314,SAR0314,putative transcription regulator,1,0,0,C,SNP,0,C,1,C,1,1
P040,360733,360733,,G,T,CCA,ACA,Non-synonymous,Altering,SAR0316,SAR0316,putative membrane protein,1,0,0,C,SNP,0,G,1,T,1,1
P040,464856,464856,,G,T,GGT,GTT,Non-synonymous,Altering,SAR0435,SAR0435,exotoxin,1,0,0,C,SNP,0,G,1,G,1,1
P040,476421,476421,,C,G,ACA,AGA,Non-synonymous,Altering,SAR0450,SAR0450,putative cobalamin synthesis protein,1,0,0,C,SNP,0,C,1,C,1,1
P040,503106,503106,,T,G,ATC,AGC,Non-synonymous,Altering,SAR0471,SAR0471,"glutamate synthase, large subunit",1,0,0,C,SNP,0,T,1,NA,NA,1
P040,512460,512460,,T,C,GGT,GGC,Synonymous,Silent,SAR0478,SAR0478,conserved hypothetical protein,1,0,0,C,SNP,0,T,1,T,1,1
P040,599971,599971,,T,C,GTA,GCA,Non-synonymous,Altering,SAR0552,SAR0552,translation elongation factor G,1,0,0,C,SNP,0,T,1,T,1,1
P040,642148,642148,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P040,653128,653128,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P040,680279,680279,,G,A,GTA,ATA,Non-synonymous,Altering,SAR0633,SAR0633,putative NADH-Ubiquinone/plastoquinone (complex I) oxidoreductase protein,1,0,0,C,SNP,0,G,1,G,1,1
P040,720969,720969,,C,T,ATC,ATT,Synonymous,Silent,SAR0673,SAR0673,conserved hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P040,806188,806188,,A,G,ACA,ACG,Synonymous,Silent,SAR0772,SAR0772,putative sulfatase,0,0,1,B,SNP,0,A,1,NA,NA,1
P040,825727,825727,,G,T,TTG,TTT,Non-synonymous,Altering,SAR0787,SAR0787,FecCD transport family protein,1,0,0,C,SNP,0,A,1,G,1,1
P040,932742,932742,,T,C,GTG,GCG,Non-synonymous,Altering,SAR0895,SAR0895,putative activated D-alanine transport protein,1,0,0,C,SNP,0,T,1,T,1,1
P040,1092666,1092666,,G,A,GAA,AAA,Non-synonymous,Altering,SAR1047,SAR1047,putative bifunctional purine biosynthesis protein [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase and IMP cyclohydrolase],1,0,0,C,SNP,0,G,1,G,1,1
P040,1158771,1158771,,G,A,GCA,ACA,Non-synonymous,Altering,SAR1112,SAR1112,putative phenylalanyl-tRNA synthetase beta chain,1,0,0,C,SNP,0,G,1,G,1,1
P040,1204501,1204501,,G,A,GAA,AAA,Non-synonymous,Altering,SAR1160,SAR1160,putative cell division protein,1,0,0,C,SNP,0,G,1,G,1,1
P040,1254011,1254011,,A,G,GAA,GGA,Non-synonymous,Altering,SAR1203,SAR1203,ATP-dependent DNA helicase,1,0,0,C,SNP,0,A,1,A,1,1
P040,1294433,1294433,,T,C,GCT,GCC,Synonymous,Silent,SAR1239,SAR1239,prolyl-tRNA synthetase,1,0,0,C,SNP,0,T,1,T,1,1
P040,1332363,1332363,,C,T,GCC,GCT,Synonymous,Silent,SAR1270,SAR1270,putative membrane protein,1,0,0,C,SNP,0,C,1,C,1,1
P040,1406246,1406246,,G,T,GAG,GAT,Non-synonymous,Altering,SAR1357,SAR1357,putative exonuclease,1,0,0,C,SNP,0,G,1,G,1,1
P040,1428825,1428825,,G,T,GAG,GAT,Non-synonymous,Altering,SAR1372,SAR1372,putative membrane protein,1,0,0,C,SNP,0,G,1,G,1,1
P040,1505593,1505593,,C,T,GTG,GTA,Synonymous,Silent,SAR1447,SAR1447,very large surface anchored protein,1,0,0,C,SNP,0,C,1,C,1,1
P040,1516381,1516381,,A,C,GTT,GTG,Synonymous,Silent,SAR1447,SAR1447,very large surface anchored protein,1,0,0,C,SNP,0,A,1,A,1,1
P040,1517978,1517978,,G,A,TCA,TTA,Non-synonymous,Altering,SAR1447,SAR1447,very large surface anchored protein,1,0,0,C,SNP,0,G,1,G,1,1
P040,1530932,1530932,,G,A,ACA,ATA,Non-synonymous,Altering,SAR1447,SAR1447,very large surface anchored protein,1,0,0,C,SNP,0,G,1,G,1,1
P040,2147436,2147436,,G,A,ACA,ATA,Non-synonymous,Altering,SAR2062,SAR2062,putative Clp protease,0,0,1,B,SNP,0,G,1,G,1,1
P040,2194552,2194552,,G,A,GAC,GAT,Synonymous,Silent,SAR2133,SAR2133,conserved hypothetical protein,1,0,0,C,SNP,0,G,1,G,1,1
P040,2233873,2233873,,T,C,ACA,GCA,Non-synonymous,Altering,SAR2165,SAR2165,putative potassium-transporting ATPase a chain,1,0,0,C,SNP,0,T,1,T,1,1
P040,2276439,2276439,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P040,2406390,2406390,,G,A,AGC,AGT,Synonymous,Silent,SAR2334,SAR2334,50S ribosomal protein L4,1,0,0,C,SNP,0,G,1,G,1,1
P040,2445483,2445483,,G,A,GGT,GAT,Non-synonymous,Altering,SAR2377,SAR2377,urease accessory protein UreG,1,0,0,C,SNP,0,G,1,G,1,1
P040,2512511,2512511,,A,G,ATG,ACG,Non-synonymous,Altering,SAR2442,SAR2442,teicoplanin resistance associated membrane protein,1,0,0,C,SNP,0,A,1,A,1,1
P040,2625343,2625343,,C,T,ATG,ATA,Non-synonymous,Altering,SAR2543,SAR2543,putative membrane protein,1,0,0,C,SNP,0,C,1,C,1,1
P040,2691530,2691530,,G,T,TCT,TAT,Non-synonymous,Altering,SAR2607,SAR2607,putative haloacid dehalogenase-like hydrolase,1,0,0,C,SNP,0,G,1,G,1,1
P040,2734044,2734044,,G,A,CCT,TCT,Non-synonymous,Altering,SAR2646,SAR2646,putative phytoene dehydrogenase related protein,1,0,0,C,SNP,0,G,1,G,1,1
P040,2765001,2765001,,G,C,CAT,GAT,Non-synonymous,Altering,SAR2679,SAR2679,putative alpha-acetolactate decarboxylase,1,0,0,C,SNP,0,G,1,G,1,1
P040,2766909,2766909,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P040,2775253,2775253,,G,A,CCA,CTA,Non-synonymous,Altering,SAR2687,SAR2687,putative AMP-binding enzyme,1,0,0,C,SNP,0,G,1,G,1,1
P040,2775729,2775729,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P040,2796307,2796307,,C,T,GAG,GAA,Synonymous,Silent,SAR2702,SAR2702,sensor kinase protein,1,0,0,C,SNP,0,C,1,C,1,1
P040,2816382,2816382,,C,A,CAA,AAA,Non-synonymous,Altering,SAR2719,SAR2719,transcriptional regulator (antiterminator),1,0,0,C,SNP,0,C,1,C,1,1
P040,109709(self),NA,"205644(MSSA476, BX571857.1)",T,C,ATA,ACA,Non-synonymous,Altering,SAS0174,(no ortholog),putative permease protein,1,0,0,C,SNP,0,NA,NA,C,1,1
P040,1761549(self),NA,"1886257(MSSA476, BX571857.1)",A,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,A,1,1
P040,1925075(self),NA,unknown,C,A,GTT,TTT,Non-synonymous,Altering,"(xbase, CDS NA)",(no ortholog),,1,0,0,C,SNP,0,NA,NA,C,1,1
P040,2279342(self),NA,"2420940(MSSA476, BX571857.1)",C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,C,1,1
P040,339398(self),NA,"420265(MSSA476, BX571857.1)",T,A,ATT,AAT,Non-synonymous,Altering,SAS0375,(no ortholog),hypothetical protein,1,0,0,C,SNP,0,NA,NA,A,1,1
P040,554602(self),NA,"638017(MSSA476, BX571857.1)",A,G,AAA,GAA,Non-synonymous,Altering,SAS0557,(no ortholog),hypothetical protein,1,0,0,C,SNP,0,NA,NA,G,1,1
P040,k31_var_129,1967834,,A,AA,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,A,1,1
P040,k31_var_138,2152570,,G,GG,ACC,ACG,"Frameshift, stop gained",Truncating,SAR2070,SAR2070,hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,G,1,1
P040,k31_var_140,NA,"2023151(MSSA476, BX571857.1)",AT,A,AAT,AAT,Frameshift with readthrough,Altering,SAS1861,SAR2030,protein map (MHC analogous protein),1,0,0,C,ShINDEL,1,NA,NA,AT,1,1
P040,k31_var_141,NA,"2420273(MSSA476, BX571857.1)",T,TA,ATC,ACA,"Frameshift, stop gained",Truncating,SAS2262,(no ortholog),MFS transporter,1,0,0,C,ShINDEL,1,NA,NA,T,1,1
P040,k31_var_146,2829592,,A,AA,TTT,TTG,"Frameshift, stop gained",Truncating,SAR2726,SAR2726,conserved hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,AA,1,1
P040,k31_var_151,2608889,,TT,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,T,1,1
P040,k31_var_159,NA,"85549(MSSA476, BX571857.1)",G,GA,CTA,ACT,"Frameshift, stop gained",Truncating,SAS0077,(no ortholog),hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,G,1,1
P040,k31_var_162,2701823,,A,AC,GGG,GGT,"Frameshift, stop gained",Truncating,glcB,SAR2618,"PTS system, glucose-specific IIABC component",1,0,0,C,ShINDEL,1,NA,NA,A,1,1
P040,k31_var_163,16070,,GT,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,GT,1,1
P040,k31_var_172,2383390,,CT,C,GTA,GTG,"Frameshift, stop gained",Truncating,SAR2297,SAR2297,acetolactate synthase,1,0,0,C,ShINDEL,1,NA,NA,CT,1,1
P040,k31_var_173,1913255,,TT,T,AAT,AAA,"Frameshift, stop gained",Truncating,SAR1830,SAR1830,beta-lactam sensor/signal transducer BlaR1,1,0,0,C,ShINDEL,1,NA,NA,TT,1,1
P040,k31_var_195,1179657,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,A,1,1
P040,k31_var_199,2852703,,AA,A,AGT,GTG,"Frameshift, stop gained",Truncating,icaA,SAR2747,glucosaminyltransferase,1,0,0,C,ShINDEL,1,NA,NA,AA,1,1
P040,k31_var_24,NA,"642592(MSSA476, BX571857.1)",A,AA,AAT,AAA,"Frameshift, stop gained",Truncating,SAS0075,(no ortholog),membrane protein,1,0,0,C,ShINDEL,1,NA,NA,NA,NA,NA
P040,k31_var_49,2445302,,A,ATA,GAT,GTA,"Frameshift, stop gained",Truncating,ureG,SAR2377,urease accessory protein UreG,0,0,1,B,ShINDEL,2,NA,NA,NA,1,1
P040,k61_var_110,815827,,G,GCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGG,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,56,NA,NA,GCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGG,1,1
P040,k61_var_112,891032,,G,GATAGTGACTCGGATTCAG,GCG,GAT,"Non-synonymous, 6 codon deletion",Altering,SAR0842,SAR0842,clumping factor A,1,0,0,C,ShINDEL,18,NA,NA,GATAGTGACTCGGATTCAG,1,1
P040,k61_var_120,2425118,,C,CCCAACTTGCACATTATTGTAAGCTGACTTTTCGTCACCTTCTATGTTGGGGCCCCG,GCG,GCG,"Frameshift, stop gained",Truncating,SAR_RS12300,(no ortholog),nitrogen fixation protein NifR,1,0,0,C,ShINDEL,56,NA,NA,CCCAACTTGCACATTATTGTAAGCTGACTTTTCGTCACCTTCTATGTTGGGGCCCCG,1,1
P040,k61_var_183,2580800,,A,AACTAATGCGTTCCTTTATTTTCTGCGAATTTTATGAGCTAGAAAGGCGCCCAACTCTCCCTGTTTGTTAACTTTCGCCTCGAAAGTTTCTATGTTGGGACCCTATGCATTAGTAGCGAAGCTA,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,123,NA,NA,NA,NA,NA
P040,k61_var_5,2488248,,CGT,CTC,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,NA,NA,NA
P041,838015,838015,,G,A,CCT,CTT,Non-synonymous,Altering,SAR0800,SAR0800,putative membrane protein,1,0,0,C,SNP,0,G,1,G,1,1
P041,2781152,2781152,,C,A,GCG,GAG,Non-synonymous,Altering,SAR2692,SAR2692,conserved hypothetical protein,0,0,1,B,SNP,0,C,1,C,1,1
P041,2860228,2860228,,A,C,GGT,GGG,Synonymous,Silent,SAR2755,SAR2755,HisF cyclase-like protein,0,0,1,B,SNP,0,A,1,A,1,1
P041,1818909(self),NA,"1900526(MSSA476, BX571857.1)",G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,NA,NA,NA
P042,7048,7048,,C,T,ACC,ATC,Non-synonymous,Altering,SAR0006,SAR0006,DNA gyrase subunit A,1,0,0,C,SNP,0,C,1,NA,NA,1
P042,115957,115957,,A,C,AAA,CAA,Non-synonymous,Altering,SAR0109,SAR0109,putative transporter protein,0,0,1,B,SNP,0,C,1,NA,NA,1
P042,396719,396719,,C,T,GAA,AAA,Non-synonymous,Altering,SAR0352,SAR0352,conserved hypothetical protein,0,0,1,B,SNP,0,C,1,C,1,1
P042,806071,806071,,T,G,GGT,GGG,Synonymous,Silent,SAR0772,SAR0772,putative sulfatase,0,0,1,B,SNP,0,T,1,T,1,1
P042,947195,947195,,G,A,TCG,TTG,Non-synonymous,Altering,SAR0913,SAR0913,Na+/H+ antiporter subunit,0,0,1,B,SNP,0,G,1,G,1,1
P042,1523100,1523100,,G,A,CAA,TAA,Nonsense,Truncating,SAR1447,SAR1447,very large surface anchored protein,1,0,0,C,SNP,0,G,1,G,1,1
P042,1727130,1727130,,G,A,CAA,TAA,Nonsense,Truncating,SAR1659,SAR1659,heat-inducible transcription repressor,1,0,0,C,SNP,0,G,1,G,1,1
P042,1962252,1962252,,T,C,ATA,GTA,Non-synonymous,Altering,SAR1874,SAR1874,conserved hypothetical protein,1,0,0,C,SNP,0,T,1,T,1,1
P042,2186761,2186761,,C,T,CGT,TGT,Non-synonymous,Altering,SAR2126,SAR2126,autoinducer sensor protein response regulator protein,1,0,0,C,SNP,0,C,1,C,1,1
P042,2632443,2632443,,G,A,CAA,TAA,Nonsense,Truncating,SAR2550,SAR2550,oligopeptide transporter putative ATPase domain,1,0,0,C,SNP,0,G,1,G,1,1
P042,2748624,2748624,,G,A,CGC,CAC,Non-synonymous,Altering,SAR2661,SAR2661,putative hydrolase,0,0,1,B,SNP,0,G,1,G,1,1
P042,2841054,2841054,,T,A,TAT,TTT,Non-synonymous,Altering,SAR2734,SAR2734,serine-rich adhesin for platelets,0,0,1,B,SNP,0,A,1,NA,NA,1
P042,k31_var_182,1576358,,T,TT,AAT,AAA,"Frameshift, stop gained",Truncating,gpsA,SAR1483,glycerol-3-phosphate dehydrogenase [NAD(P)+],1,0,0,C,ShINDEL,1,NA,NA,T,1,1
P042,k31_var_20,2185917,,T,TG,GAT,CGA,"Frameshift, stop gained",Truncating,agrC,SAR2125,accessory gene regulator protein C,1,0,0,C,ShINDEL,1,NA,NA,T,1,1
P042,k31_var_35,2186499,,C,CGC,CGC,GCC,"Frameshift, stop gained",Truncating,agrA,SAR2126,autoinducer sensor protein response regulator protein,0,0,1,B,ShINDEL,2,NA,NA,C,1,1
P043,15989,15989,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,G,1,G,1,1
P043,2543577,2543577,,C,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,1,C,1,1
P043,k31_var_98,2193759,,C,CC,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,C,1,1
P045,773642,773642,,G,T,ATG,ATT,Non-synonymous,Altering,SAR0738,SAR0738,ABC transporter ATP-binding protein,0,0,1,B,SNP,0,G,1,G,1,1
P046,66304,66304,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,0,G,0,0
P046,391838,391838,,A,G,AAA,GAA,Non-synonymous,Altering,SAR0348,SAR0348,ABC transporter ATP-binding protein,0,0,1,B,SNP,0,A,1,A,1,1
P046,598600,598600,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,0,A,0,0
P046,603737,603737,,T,C,AAC,AGC,Non-synonymous,Altering,SAR0554,SAR0554,putative peptidase,0,0,1,B,SNP,0,T,0,T,0,0
P046,640589,640589,,G,A,GAA,AAA,Non-synonymous,Altering,SAR0589,SAR0589,putative amino acid permease,0,0,1,B,SNP,0,G,1,NA,NA,1
P046,651287,651287,,A,G,TAT,TAC,Synonymous,Silent,SAR0600,SAR0600,pyridine nucleotide-disulphide oxidoreductase protein,0,0,1,B,SNP,0,A,0,A,0,0
P046,797316,797316,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,1,A,1,1
P046,849469,849469,,T,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,T,1,1
P046,931531,931531,,C,T,GCG,GTG,Non-synonymous,Altering,SAR0894,SAR0894,D-alanine-D-alanyl carrier protein ligase,0,0,1,B,SNP,0,C,0,C,0,0
P046,942138,942138,,C,T,TTC,TTT,Synonymous,Silent,SAR0905,SAR0905,putative transporter protein,0,0,1,B,SNP,0,C,1,C,1,1
P046,968950,968950,,A,C,GAA,GCA,Non-synonymous,Altering,SAR0929,SAR0929,conserved hypothetical protein,0,0,1,B,SNP,0,A,0,A,0,0
P046,1012090,1012090,,C,T,TCA,TTA,Non-synonymous,Altering,SAR0968,SAR0968,putative oligopeptidase,0,0,1,B,SNP,0,C,1,C,1,1
P046,1100344,1100344,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,1,C,1,1
P046,1152316,1152316,,T,C,GCT,GCC,Synonymous,Silent,SAR1106,SAR1106,putative transport system extracellular binding lipoprotein,0,0,1,B,SNP,0,T,0,T,0,0
P046,1260779,1260779,,A,G,AAC,AGC,Non-synonymous,Altering,SAR1210,SAR1210,putative chromosome partition protein,0,0,1,B,SNP,0,A,1,A,1,1
P046,1332844,1332844,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,0,G,0,0
P046,1337777,1337777,,G,A,GTA,ATA,Non-synonymous,Altering,SAR1273,SAR1273,putative glycerol uptake operon antiterminator regulatory protein,0,0,1,B,SNP,0,G,1,G,1,1
P046,1350339,1350339,,A,G,CAA,CGA,Non-synonymous,Altering,SAR1284,SAR1284,glutamine synthetase,0,0,1,B,SNP,0,A,1,A,1,1
P046,1402472,1402472,,C,G,GCT,GGT,Non-synonymous,Altering,SAR1352,SAR1352,putative transketolase,0,0,1,B,SNP,0,C,0,C,0,0
P046,1447668,1447668,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,T,1,1
P046,1456409,1456409,,T,C,GAC,GGC,Non-synonymous,Altering,SAR1399,SAR1399,ABC transporter ATP-binding protein,0,0,1,B,SNP,0,T,1,T,1,1
P046,1459625,1459625,,T,C,GAA,GGA,Non-synonymous,Altering,SAR1402,SAR1402,phosphate-binding lipoprotein,1,0,0,C,SNP,0,T,1,T,1,1
P046,1482403,1482403,,A,G,TTA,CTA,Synonymous,Silent,SAR1424,SAR1424,dihydrolipoamide succinyltransferase E2 component of 2-oxoglutarate dehydrogenase complex,0,0,1,B,SNP,0,A,0,A,0,0
P046,1492631,1492631,,G,A,ACT,ATT,Non-synonymous,Altering,SAR1432,SAR1432,putative protease,0,0,1,B,SNP,0,G,1,G,1,1
P046,1661421,1661421,,G,A,GCT,GTT,Non-synonymous,Altering,SAR1589,SAR1589,"6-phosphogluconate dehydrogenase, decarboxylating",0,0,1,B,SNP,0,G,1,G,1,1
P046,1733025,1733025,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,0,A,0,0
P046,1805787,1805787,,G,A,GCC,GTC,Non-synonymous,Altering,SAR1743,SAR1743,valyl-tRNA synthetase,0,0,1,B,SNP,0,G,0,G,0,0
P046,1830229,1830229,,T,C,ATT,GTT,Non-synonymous,Altering,SAR1766,SAR1766,glyceraldehyde 3-phosphate dehydrogenase 2,0,0,1,B,SNP,0,T,1,T,1,1
P046,1838452,1838452,,G,A,GCA,GTA,Non-synonymous,Altering,SAR1771,SAR1771,alkaline phosphatase synthesis sensor protein,0,0,1,B,SNP,0,G,1,NA,NA,1
P046,1927350,1927350,,G,A,CAA,TAA,Nonsense,Truncating,SAR1841,SAR1841,putative surface anchored protein,0,0,1,B,SNP,0,G,0,T,0,0
P046,1969401,1969401,,G,T,ATG,ATT,Non-synonymous,Altering,SAR1883,SAR1883,hypothetical protein,0,0,1,B,SNP,0,G,0,G,0,0
P046,2262327,2262327,,T,A,ATT,TTT,Non-synonymous,Altering,SAR2193,SAR2193,ATP synthase alpha chain,0,0,1,B,SNP,0,T,0,T,0,0
P046,2274738,2274738,,C,T,GAA,AAA,Non-synonymous,Altering,SAR2208,SAR2208,putative 50S ribosomal protein L31,0,0,1,B,SNP,0,C,1,NA,NA,1
P046,2314341,2314341,,C,T,GAC,GAT,Synonymous,Silent,SAR2245,SAR2245,putative transcriptional antiterminator,0,0,1,B,SNP,0,C,1,C,1,1
P046,2360992,2360992,,C,T,GCA,ACA,Non-synonymous,Altering,SAR2277,SAR2277,putative zinc-binding dehydrogenase,0,0,1,B,SNP,0,C,1,C,1,1
P046,2383097,2383097,,T,C,TCA,TCG,Synonymous,Silent,SAR2297,SAR2297,putative acetolactate synthase,0,0,1,B,SNP,0,T,1,NA,NA,1
P046,2418621,2418621,,C,G,GCA,CCA,Non-synonymous,Altering,SAR2345,SAR2345,AcrB/AcrD/AcrF family protein,0,0,1,B,SNP,0,C,0,C,0,0
P046,2590757,2590757,,T,C,ACC,GCC,Non-synonymous,Altering,SAR2516,SAR2516,putative adenosylmethionine-8-amino-7-oxononanoate aminotransferase,0,0,1,B,SNP,0,T,1,T,1,1
P046,2661257,2661257,,T,A,CAA,CAT,Non-synonymous,Altering,SAR2580,SAR2580,fibronectin-binding protein precursor,0,0,1,B,SNP,0,A,1,A,1,1
P046,2663612,2663612,,C,G,AAG,AAC,Non-synonymous,Altering,SAR2580,SAR2580,fibronectin-binding protein precursor,0,0,1,B,SNP,0,C,0,C,0,0
P046,2688635,2688635,,G,T,GCC,GCA,Synonymous,Silent,SAR2603,SAR2603,NAD(P)H-dependent oxidoreductase,0,0,1,B,SNP,0,G,0,G,0,0
P046,2720215,2720215,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,NA,NA,1
P046,2763487,2763487,,T,C,ATT,ACT,Non-synonymous,Altering,SAR2678,SAR2678,putative ketopantoate reductase,0,0,1,B,SNP,0,T,0,T,0,0
P046,2792732,2792732,,T,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,T,1,1
P046,2803109,2803109,,G,A,GCA,GTA,Non-synonymous,Altering,SAR2709,SAR2709,clumping factor B,0,0,1,B,SNP,0,G,0,G,0,0
P046,2827791,2827791,,T,C,ATG,GTG,Non-synonymous,Altering,SAR2725,SAR2725,putative surface anchored protein,0,0,1,B,SNP,0,T,0,T,0,0
P046,2852724,2852724,,C,A,GGC,GGA,Synonymous,Silent,SAR2747,SAR2747,glucosaminyltransferase,0,0,1,B,SNP,0,C,0,NA,NA,0
P046,1888828(self),NA,"1898796(MSSA476, BX571857.1)",T,C,ATG,GTG,Non-synonymous,Altering,SAS1748,SAR2511,gamma-hemolysin component B precursor,0,0,1,B,SNP,0,NA,NA,T,1,1
P046,2057525(self),NA,"2073083(MSSA476, BX571857.1)",C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,C,0,0
P046,2209059(self),2331743,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,NA,NA,NA
P046,2557490(self),NA,"2587698(MSSA476, BX571857.1)",G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,G,1,1
P046,299781(self),NA,"276184(MSSA476, BX571857.1)",A,C,AAA,ACA,Non-synonymous,Altering,SAS0232,SAR0252,2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase,0,0,1,B,SNP,0,NA,NA,C,0,0
P046,339958(self),NA,"316306(MSSA476, BX571857.1)",C,T,GTA,GCA,Non-synonymous,Altering,SAS0268,(no ortholog),hypothetical protein,0,0,1,B,SNP,0,NA,NA,C,0,0
P046,345306(self),NA,"321654(MSSA476, BX571857.1)",C,T,ATG,ACG,Non-synonymous,Altering,SAS0274,SAR0294,hypothetical protein,0,0,1,B,SNP,0,NA,NA,NA,NA,NA
P046,346829(self),NA,"323177(MSSA476, BX571857.1)",A,T,TTA,ATA,Non-synonymous,Altering,SAS0277,(no ortholog),hypothetical protein,0,0,1,B,SNP,0,NA,NA,NA,NA,NA
P046,649197(self),NA,"620215(MSSA476, BX571857.1)",T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,T,1,1
P046,91272(self),NA,"70769(MSSA476, BX571857.1)",G,T,ATC,CTC,Non-synonymous,Altering,SAS0062,(no ortholog),hypothetical protein,0,0,1,B,SNP,0,NA,NA,T,1,1
P046,k31_var_15,388089,,TC,T,CTA,TAG,Nonsense,Truncating,SAR0342,SAR0342,hypothetical protein,0,0,1,B,ShINDEL,1,NA,NA,TC,0,0
P046,k31_var_19,2802360,,TT,T,AAG,AGC,"Frameshift, stop gained",Truncating,SAR2709,SAR2709,clumping factor B,0,0,1,B,ShINDEL,1,NA,NA,TT,1,1
P046,k31_var_21,1415428,,T,TA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,T,1,1
P046,k31_var_37,1887180,,A,AA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,A,1,1
P046,k31_var_42,1167113,,T,TA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,TA,0,0
P046,k31_var_71,937800,,AA,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,NA,NA,NA
P046,k31_var_73,NA,"1793286(71193, NC_017673.1)",TTGAAACGAG,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,9,NA,NA,NA,NA,NA
P046,k31_var_75,1939013,,TT,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,TT,1,1
P046,k61_var_35,NA,"2700005(MSSA476, BX571857.1)",TATCCGAGTCTGAGTCGCT,T,AGC,ATC,"Non-synonymous, 6 codon deletion",Altering,SAS2516,SAR2709,clumping factor B,0,0,1,B,ShINDEL,18,NA,NA,TATCCGAGTCTGAGTCGCT,0,0
P046,k61_var_72,124292,,C,CGTCTTCTTTGCCAGGCTTGTTGTT,GGC,GGT,"Non-synonymous, 8 codon insertion",Altering,SAR0114,SAR0114,immunoglobulin G binding protein A precursor,0,0,1,B,ShINDEL,24,NA,NA,C,1,1
P047,2035892,2035892,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P048,143425,143425,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,0,C,0,0
P048,223455,223455,,T,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,T,1,1
P048,323292,323292,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,1,C,1,1
P048,348380,348380,,A,T,ATA,ATT,Synonymous,Silent,SAR0305,SAR0305,putative membrane protein,0,0,1,B,SNP,0,T,1,T,1,1
P048,356887,356887,,T,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,1,A,1,1
P048,428137,428137,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,0,G,0,0
P048,435953,435953,,G,A,GAT,AAT,Non-synonymous,Altering,SAR0400,SAR0400,nitroreductase family protein,0,0,1,B,SNP,0,G,0,NA,NA,0
P048,554865,554865,,A,G,AAA,GAA,Non-synonymous,Altering,SAR0515,SAR0515,dihydropteroate synthase,0,0,1,B,SNP,0,A,1,A,1,1
P048,690125,690125,,G,T,ACC,ACA,Synonymous,Silent,SAR0643,SAR0643,ABC transporter ATP-binding protein,0,0,1,B,SNP,0,G,1,G,1,1
P048,719139,719139,,G,A,ACG,ACA,Synonymous,Silent,SAR0672,SAR0672,putative ABC transporter permease,0,0,1,B,SNP,0,G,0,G,0,0
P048,722964,722964,,G,A,GCA,GTA,Non-synonymous,Altering,SAR0675,SAR0675,putative exported protein,0,0,1,B,SNP,0,G,0,G,0,0
P048,749653,749653,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,0,NA,NA,0
P048,844477,844477,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,1,G,1,1
P048,875770,875770,,G,A,GGT,GAT,Non-synonymous,Altering,SAR0830,SAR0830,triosephosphate isomerase,0,0,1,B,SNP,0,G,1,NA,NA,1
P048,888799,888799,,T,A,AAT,AAA,Non-synonymous,Altering,SAR0842,SAR0842,clumping factor A,0,0,1,B,SNP,0,T,1,T,1,1
P048,888990,888990,,C,T,CCG,CTG,Non-synonymous,Altering,SAR0842,SAR0842,clumping factor A,0,0,1,B,SNP,0,C,1,C,1,1
P048,913327,913327,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P048,919034,919034,,A,G,ATG,GTG,Non-synonymous,Altering,SAR0880,SAR0880,conserved hypothetical protein,0,0,1,B,SNP,0,A,0,A,0,0
P048,923667,923667,,G,C,GGT,GCT,Non-synonymous,Altering,SAR0885,SAR0885,putative membrane protein,0,0,1,B,SNP,0,G,0,G,0,0
P048,979109,979109,,T,C,GAT,GAC,Synonymous,Silent,SAR0937,SAR0937,putative membrane protein,0,0,1,B,SNP,0,T,1,T,1,1
P048,988145,988145,,C,T,CCT,TCT,Non-synonymous,Altering,SAR0944,SAR0944,putative exported protein,0,0,1,B,SNP,0,C,1,C,1,1
P048,1208301,1208301,,G,A,GGA,AGA,Non-synonymous,Altering,SAR1162,SAR1162,cell division protein FtsZ,0,0,1,B,SNP,0,G,1,G,1,1
P048,1244444,1244444,,A,G,ATA,ATG,Non-synonymous,Altering,SAR1196,SAR1196,serine/threonine-protein kinase,0,0,1,B,SNP,0,A,0,A,0,0
P048,1251330,1251330,,A,G,GAA,GAG,Synonymous,Silent,SAR1202,SAR1202,conserved hypothetical protein,1,0,0,C,SNP,0,A,1,A,1,1
P048,1267080,1267080,,C,T,GGC,GGT,Synonymous,Silent,SAR1216,SAR1216,putative tRNA (guanine-7-)-methyltransferase,0,0,1,B,SNP,0,C,1,C,1,1
P048,1443179,1443179,,A,G,GAA,GGA,Non-synonymous,Altering,SAR1385,SAR1385,tryptophan synthase beta chain,0,0,1,B,SNP,0,A,1,NA,NA,1
P048,1459203,1459203,,C,T,GCT,ACT,Non-synonymous,Altering,SAR1402,SAR1402,phosphate-binding lipoprotein,1,0,0,C,SNP,0,C,1,C,1,1
P048,1534125,1534125,,G,A,CAA,TAA,Nonsense,Truncating,SAR1447,SAR1447,very large surface anchored protein,0,1,0,D,SNP,0,G,1,G,1,1
P048,1548959,1548959,,C,T,GAA,AAA,Non-synonymous,Altering,SAR1456,SAR1456,conserved hypothetical protein,0,0,1,B,SNP,0,C,1,C,1,1
P048,1550698,1550698,,T,C,CGA,CGG,Synonymous,Silent,SAR1459,SAR1459,conserved hypothetical protein,1,0,0,C,SNP,0,T,1,T,1,1
P048,1685806,1685806,,G,A,CCA,TCA,Non-synonymous,Altering,SAR1613,SAR1613,putative glycine cleavage system P-protein,0,0,1,B,SNP,0,G,1,G,1,1
P048,1704931,1704931,,G,A,ACA,ATA,Non-synonymous,Altering,SAR1636,SAR1636,conserved hypothetical protein,1,0,0,C,SNP,0,G,1,G,1,1
P048,1757108,1757108,,C,T,GCA,ACA,Non-synonymous,Altering,SAR1697,SAR1697,putative alanyl-tRNA synthetase,0,0,1,B,SNP,0,C,0,C,0,0
P048,1763273,1763273,,T,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,0,T,0,0
P048,1785576,1785576,,G,A,ACC,ACT,Synonymous,Silent,SAR1719,SAR1719,queuine tRNA-ribosyltransferase,0,0,1,B,SNP,0,G,1,NA,NA,1
P048,1791857,1791857,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,A,1,A,1,1
P048,1808956,1808956,,T,C,AAT,GAT,Non-synonymous,Altering,SAR1745,SAR1745,putative membrane protein,1,0,0,C,SNP,0,T,1,T,1,1
P048,1922338,1922338,,C,T,GTG,GTA,Synonymous,Silent,SAR1839,SAR1839,putative polysaccharide biosynthesis protein,0,0,1,B,SNP,0,T,1,T,1,1
P048,2023130,2023130,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,1,G,1,1
P048,2052419,2052419,,A,G,TAT,TAC,Synonymous,Silent,SAR1960,SAR1960,putative membrane protein,0,0,1,B,SNP,0,A,1,NA,NA,1
P048,2065333,2065333,,T,C,GAT,GGT,Non-synonymous,Altering,SAR1975,SAR1975,histidine kinase sensor,0,0,1,B,SNP,0,T,1,T,1,1
P048,2072742,2072742,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,1,C,1,1
P048,2170831,2170831,,T,C,AAT,GAT,Non-synonymous,Altering,SAR2108,SAR2108,putative leukocidin S subunit,0,0,1,B,SNP,0,T,1,T,1,1
P048,2486856,2486856,,G,A,AAC,AAT,Synonymous,Silent,SAR2417,SAR2417,urocanate hydratase,0,0,1,B,SNP,0,G,1,G,1,1
P048,2543199,2543199,,G,T,AGT,ATT,Non-synonymous,Altering,SAR2470,SAR2470,putative exported protein,0,0,1,B,SNP,0,G,0,G,0,0
P048,2556010,2556010,,G,T,ACA,AAA,Non-synonymous,Altering,SAR2484,SAR2484,respiratory nitrate reductase delta chain,0,0,1,B,SNP,0,G,0,G,0,0
P048,2607157,2607157,,G,A,ATC,ATT,Synonymous,Silent,SAR2530,SAR2530,putative membrane protein,0,0,1,B,SNP,0,G,0,G,0,0
P048,2655233,2655233,,G,A,CCA,TCA,Non-synonymous,Altering,SAR2574,SAR2574,putative helicase,0,0,1,B,SNP,0,G,0,G,0,0
P048,2732126,2732126,,A,G,GGT,GGC,Synonymous,Silent,SAR2643,SAR2643,squalene desaturase (pseudogene),0,0,1,B,SNP,0,A,1,A,1,1
P048,2744844,2744844,,G,A,CAA,TAA,Nonsense,Truncating,SAR2656,SAR2656,conserved hypothetical protein,1,0,0,C,SNP,0,G,1,G,1,1
P048,2831563,2831563,,A,G,TTT,CTT,Non-synonymous,Altering,SAR2728,SAR2728,preprotein translocase SecA subunit-like protein,0,0,1,B,SNP,0,A,1,A,1,1
P048,2901731,2901731,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,T,1,1
P048,10070(self),NA,"2558529(MSSA476,  BX571857.1)",C,T,GAT,AAT,Non-synonymous,Altering,SAS2387,SAR2580,fibronectin-binding protein precursor,0,0,1,B,SNP,0,NA,NA,C,1,1
P048,1353874(self),NA,"1134811(MSSA476, BX571857.1)",A,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,NA,NA,NA
P048,1400306(self),NA,"1181288(MSSA476, BX571857.1)",C,T,GCA,GTA,Non-synonymous,Altering,SAS1108,(no ortholog),anti protein,0,0,1,B,SNP,0,NA,NA,C,1,1
P048,2116692(self),NA,"1887067(MSSA476, BX571857.1)",A,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,A,1,1
P048,2129087(self),NA,"1899462(MSSA476, BX571857.1)",A,G,GTG,GCG,Non-synonymous,Altering,SAS1749,SAR2509,gamma-hemolysin component A precursor,0,0,1,B,SNP,0,NA,NA,A,1,1
P048,229778(self),NA,unknown,C,T,GTT,ATT,Non-synonymous,Altering,SAUSA300_2624,(no ortholog),hypothetical protein,1,0,0,C,SNP,0,NA,NA,C,1,1
P048,2317411(self),NA,"2088794(MSSA476, BX571857.1)",A,G,ATT,GTT,Non-synonymous,Altering,SAS1943,SAR2125,accessory gene regulator protein C,0,0,1,B,SNP,0,NA,NA,A,1,1
P048,294671(self),NA,"48104(MSSA476, BX571857.1)",T,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,T,1,1
P048,564888(self),NA,unknown,G,A,ACA,GCA,Non-synonymous,Altering,SAUSA300_0296,SAR0293,hypothetical protein,1,0,0,C,SNP,0,NA,NA,G,1,1
P048,708234(self),NA,"469423(MSSA476, BX571857.1)",C,A,AGC,AGA,Non-synonymous,Altering,SAS0422,SAR0464,hypothetical protein,0,0,1,B,SNP,0,NA,NA,C,1,1
P048,k31_var_106,616241,,A,AA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,AA,0,0
P048,k31_var_114,2606854,,CC,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,C,0,0
P048,k31_var_128,2842597,,AT,A,AAA,AAT,"Frameshift, stop gained",Truncating,SAR2734,SAR2734,serine-rich adhesin for platelets,0,0,1,B,SNP,1,NA,NA,A,0,0
P048,k31_var_136,2186821,,A,AA,ATA,AAA,Frameshift with readthrough,Altering,agrA,SAR2126,autoinducer sensor protein response regulator protein,0,0,1,B,ShINDEL,1,NA,NA,A,0,0
P048,k31_var_209,276260,,A,AA,TGG,TAG,"Frameshift, stop gained",Truncating,ldh1,SAR0234,L-lactate dehydrogenase,1,0,0,C,ShINDEL,1,NA,NA,A,1,1
P048,k31_var_213,1965921,,AA,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,1,NA,NA,AA,1,1
P048,k31_var_247,687745,,GTTG,GCCACA,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,2,NA,NA,GTTG,1,1
P048,k31_var_52,2212806,,AA,A,AAA,AAT,"Frameshift, stop gained",Truncating,SAR2148,SAR2148,L-threonine dehydratase biosynthetic IlvA,0,0,1,B,ShINDEL,1,NA,NA,AA,1,1
P048,k31_var_53,1488954,,T,TC,GTT,CGT,"Frameshift, stop gained",Truncating,SAR1428,SAR1428,hypothetical protein,0,0,1,B,ShINDEL,1,NA,NA,T,1,1
P048,k31_var_87,2184881,,G,C,AGT,ACT,Non-synonymous,Altering,SAR2125,SAR2125,accessory gene regulator protein C,0,0,1,B,SNP,0,NA,NA,G,1,1
P048,k31_var_95,2225589,,T,TA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,TA,0,0
P048,k31_var_99,494385,,T,TC,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,T,1,1
P048,k61_var_180,2132496,,C,CT,CAA,TCA,"Frameshift, stop gained",Truncating,SAR2047,SAR2047,hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,NA,NA,NA
P048,k61_var_32,622396,,T,A,TCT,TCA,Synonymous,Silent,SAR0567,SAR0567,bone sialoprotein-binding protein,0,0,1,B,SNP,0,NA,NA,T,1,1
P048,k61_var_50,2894538,,A,AT,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,AT,0,0
P049,683211,683211,,G,A,GGA,GAA,Non-synonymous,Altering,SAR0637,SAR0637,sodium/hydrogen exchanger family protein,1,0,0,C,SNP,0,G,1,NA,NA,1
P049,714253,714253,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,NA,NA,1
P049,1028765,1028765,,T,A,AAT,AAA,Non-synonymous,Altering,SAR0983,SAR0983,hypothetical protein,1,0,0,C,SNP,0,T,1,NA,NA,1
P049,1065757,1065757,,A,C,GAT,GAG,Non-synonymous,Altering,SAR1023,SAR1023,putative aminotransferase,1,0,0,C,SNP,0,A,1,NA,NA,1
P049,1794920,1794920,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P049,k31_var_66,2380294,,T,TA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,ShINDEL,1,NA,NA,T,1,1
P050,259314,259314,,G,A,GGT,GAT,Non-synonymous,Altering,SAR0222,SAR0222,staphylocoagulase precursor,1,0,0,C,SNP,0,G,1,G,1,1
P050,376519,376519,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P050,1126337,1126337,,C,T,TGC,TAC,Non-synonymous,Altering,SAR1080,SAR1080,conserved hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P050,1279655,1279655,,A,G,AAA,AAG,Synonymous,Silent,SAR1226,SAR1226,DNA topoisomerase I,0,1,0,D,SNP,0,A,1,A,1,1
P050,1678571,1678571,,C,T,GCT,ACT,Non-synonymous,Altering,SAR1605,SAR1605,biotin carboxyl carrier protein of acetyl-CoA carboxylase,1,0,0,C,SNP,0,C,1,C,1,1
P050,1982661,1982661,,T,C,GAA,GGA,Non-synonymous,Altering,SAR1897,SAR1897,hypothetical protein,0,0,1,B,SNP,0,T,1,T,1,1
P050,k31_var_13,745215,,G,GC,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,G,1,1
P050,k31_var_95,2847792,,T,TGTTGAT,AAA,AAA,"Non-synonymous, 2 codon insertion",Altering,SAR2742,SAR2742,acetyltransferase (GNAT) family protein,1,0,0,C,ShINDEL,6,NA,NA,T,1,1
P051,1224740,1224740,,C,A,TTC,TTA,Non-synonymous,Altering,SAR1178,SAR1178,"putative carbamoyl-phosphate synthase, pyrimidine-specific, small chain",0,0,1,B,SNP,0,C,1,C,1,1
P051,2763056,2763056,,C,T,GAG,AAG,Non-synonymous,Altering,SAR2677,SAR2677,putative 3-methyl-2-oxobutanoate hydroxymethyltransferase,1,0,0,C,SNP,0,C,1,C,1,1
P052,150385,150385,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P052,245655,245655,,G,A,ATG,ATA,Non-synonymous,Altering,SAR0211,SAR0211,conserved hypothetical protein,0,0,1,B,SNP,0,G,1,G,1,1
P052,1165450,1165450,,C,A,CTT,ATT,Non-synonymous,Altering,SAR1117,SAR1117,MutS family DNA mismatch repair protein,0,0,1,B,SNP,0,C,1,C,1,1
P052,1423116,1423116,,A,C,GTA,GTC,Synonymous,Silent,SAR1368,SAR1368,sodium:alanine symporter family protein,0,0,1,B,SNP,0,A,1,A,1,1
P052,1833947,1833947,,G,T,CTC,ATC,Non-synonymous,Altering,SAR1769,SAR1769,DNA polymerase I,0,0,1,B,SNP,0,G,0,G,0,0
P052,2154595,2154595,,G,A,AAC,AAT,Synonymous,Silent,SAR2077,SAR2077,hypothetical phage protein,1,0,0,C,SNP,0,A,1,NA,NA,1
P052,1878419(self),1986214,,C,T,GGT,AGT,Non-synonymous,Altering,SAR1900,SAR1900,serine protease (pseudogene),0,0,1,B,SNP,0,NA,NA,C,0,0
P053,1016799,1016799,,C,T,ACA,ATA,Non-synonymous,Altering,SAR0973,SAR0973,conserved hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P053,1133690,1133690,,C,T,GCT,GTT,Non-synonymous,Altering,SAR1088,SAR1088,putative pyruvate carboxylase,1,0,0,C,SNP,0,C,1,C,1,1
P053,1710227,1710227,,T,C,GTA,GTG,Synonymous,Silent,SAR1641,SAR1641,putative DNA-binding protein (pseudogene),1,0,0,C,SNP,0,T,1,NA,NA,1
P053,1715633,1715633,,T,C,AGC,GGC,Non-synonymous,Altering,SAR1648,SAR1648,PhoH-like protein,1,0,0,C,SNP,0,T,1,T,1,1
P053,k31_var_139,NA,"863646(T0131, NC_017347.1)",A,G,GAT,GAA,Non-synonymous,Altering,SAT0131_00856,(no ortholog),hypothetical protein with HTH-XRE region,0,1,0,D,SNP,0,NA,NA,A,1,1
P053,k31_var_22,2109369,,TT,T,TTT,TTG,"Frameshift, stop gained",Truncating,SAR2015,SAR2015,hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,TT,1,1
P054,381211,381211,,T,G,TTG,GTG,Non-synonymous,Altering,SAR0335,SAR0335,putative luciferase-like monooxygenase,1,0,0,C,SNP,0,T,1,T,1,1
P054,960557,960557,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,G,1,G,1,1
P054,1073972,1073972,,T,G,AAT,CAT,Non-synonymous,Altering,SAR1029,SAR1029,putative exported protein,1,0,0,C,SNP,0,T,1,T,1,1
P054,1209058,1209058,,G,A,GCG,GCA,Synonymous,Silent,SAR1163,SAR1163,conserved hypothetical protein,0,1,0,D,SNP,0,G,1,G,1,1
P054,1281339,1281339,,A,C,AAA,ACA,Non-synonymous,Altering,SAR1227,SAR1227,conserved hypothetical protein,1,0,0,C,SNP,0,A,1,A,1,1
P054,1924267,1924267,,C,A,TTG,TTT,Non-synonymous,Altering,SAR1841,SAR1841,putative surface anchored protein,0,1,0,D,SNP,0,C,1,C,1,1
P054,1941694,1941694,,T,C,GCA,GCG,Synonymous,Silent,SAR1851,SAR1851,riboflavin biosynthesis protein,1,0,0,C,SNP,0,T,1,T,1,1
P054,2330714,2330714,,C,T,GTT,ATT,Non-synonymous,Altering,SAR2255,SAR2255,arginase,1,0,0,C,SNP,0,C,1,C,1,1
P054,2550252,2550252,,G,A,GGC,GGT,Synonymous,Silent,SAR2476,SAR2476,nitrite transport protein,1,0,0,C,SNP,0,G,1,G,1,1
P054,2639478,2639478,,T,C,GCA,GCG,Synonymous,Silent,SAR2557,SAR2557,conserved hypothetical protein,0,1,0,D,SNP,0,T,1,T,1,1
P054,234212(self),NA,unknown,A,C,AAT,ACT,Non-synonymous,Altering,SAR0294,SAR0294,hypothetical protein,1,0,0,C,SNP,0,NA,NA,NA,NA,NA
P054,778213(self),911230,,T,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,T,1,1
P054,k31_var_109,2190911,,G,GTA,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,2,NA,NA,G,1,1
P054,k31_var_116,1803100,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,NA,NA,T,1,1
P054,k31_var_117,2542903,,T,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,NA,NA,T,1,1
P054,k31_var_39,2122250,,T,TT,AAT,AAA,"Frameshift, stop gained",Truncating,SAR2030,SAR2030,protein map (MHC analogous protein),1,0,0,C,ShINDEL,1,NA,NA,NA,NA,NA
P054,k31_var_43,1954776,,T,TA,CTT,CTA,"Frameshift, stop gained",Truncating,SAR1866,SAR1866,camphor resistance protein CrcB,1,0,0,C,ShINDEL,1,NA,NA,T,1,1
P054,k31_var_83,1447505,,CAAAACGTGATGAGTAATTGGTTTAATGAAACATAACATGAATGTAAATTTAGCATACTGACATAAACACTACACAAACATACAGTTATATAAGTCCCCT,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,99,NA,NA,CAAAACGTGATGAGTAATTGGTTTAATGAAACATAACATGAATGTAAATTTAGCATACTGACATAAACACTACACAAACATACAGTTATATAAGTCCCCT,1,1
P054,k61_var_34,622399,,A,C,GAA,GAC,Non-synonymous,Altering,SAR0567,SAR0567,bone sialoprotein-binding protein,1,0,0,C,SNP,0,NA,NA,C,1,1
P055,409588,409588,,G,A,GCT,GTT,Non-synonymous,Altering,SAR0365,SAR0365,hypothetical protein,1,0,0,C,SNP,0,G,1,G,1,1
P055,575502,575502,,C,T,CGA,TGA,Nonsense,Truncating,SAR0528,SAR0528,putative stress response-related Clp ATPase,0,1,0,D,SNP,0,C,1,C,1,1
P055,625741,625741,,G,C,CGT,GGT,Non-synonymous,Altering,SAR0569,SAR0569,putative glycosyl transferase,1,0,0,C,SNP,0,G,1,G,1,1
P055,699971,699971,,T,C,ATG,ACG,Non-synonymous,Altering,SAR0653,SAR0653,ABC transporter ATP-binding protein,1,0,0,C,SNP,0,T,1,T,1,1
P055,1179959,1179959,,A,G,GTT,GTC,Synonymous,Silent,SAR1134,SAR1134,hypothetical protein,1,0,0,C,SNP,0,A,1,A,1,1
P055,1470201,1470201,,C,T,CAT,TAT,Non-synonymous,Altering,SAR1411,SAR1411,putative alanine racemase,1,0,0,C,SNP,0,C,1,C,1,1
P055,1503665,1503665,,A,G,ATT,ACT,Non-synonymous,Altering,SAR1447,SAR1447,very large surface anchored protein,1,0,0,C,SNP,0,A,1,A,1,1
P055,2192168,2192168,,A,G,AAT,AAC,Synonymous,Silent,SAR2130,SAR2130,ammonium transporter family protein,1,0,0,C,SNP,0,A,1,A,1,1
P055,2348858,2348858,,G,A,CCT,TCT,Non-synonymous,Altering,SAR2267,SAR2267,FecCD transport family protein,1,0,0,C,SNP,0,G,1,G,1,1
P055,2529205,2529205,,T,C,GCA,GCG,Synonymous,Silent,SAR2458,SAR2458,acetyltransferase (GNAT) family protein,1,0,0,C,SNP,0,T,1,T,1,1
P055,k31_var_110,2664074,,TTAAAACAACATACTAAACGTTTCATAATTATCGCCTGTACAATACGCACAAAAACATGTCTTGAAACGCCTTTCATTACAC,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,ShINDEL,81,NA,NA,TTAAAACAACATACTAAACGTTTCATAATTATCGCCTGTACAATACGCACAAAAACATGTCTTGAAACGCCTTTCATTACAC,1,1
P055,k31_var_3,447117,,GG,G,ACC,ACT,"Frameshift, stop gained",Truncating,SAR0411,SAR0411,hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,GG,1,1
P055,k31_var_56,492925,,AA,A,AAA,AAG,"Frameshift, stop gained",Truncating,SAR0464,SAR0464,hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,AA,1,1
P055,k31_var_70,911229,,TT,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,T,1,1
P055,k31_var_89,2663974,,AAATT,A,GAA,GTA,"Frameshift, stop gained",Truncating,SAR2581,SAR2581,hypothetical protein,0,1,0,D,ShINDEL,4,NA,NA,AAATT,1,1
P056,402299,402299,,G,A,CAG,TAG,Nonsense,Truncating,SAR0355,SAR0355,Cys/Met metabolism PLP-dependent enzyme,1,0,0,C,SNP,0,G,1,G,1,1
P056,1050307,1050307,,A,T,AAA,TAA,Nonsense,Truncating,SAR1004,SAR1004,ABC transporter ATP-binding protein,1,0,0,C,SNP,0,A,1,A,1,1
P056,1874132,1874132,,A,T,TTA,TTT,Non-synonymous,Altering,SAR1800,SAR1800,putative soluble hydrogenase subunit,1,0,0,C,SNP,0,A,1,A,1,1
P056,2690105,2690105,,A,C,GAT,GCT,Non-synonymous,Altering,SAR2605,SAR2605,D-specific D-2-hydroxyacid dehydrogenas,1,0,0,C,SNP,0,A,1,C,1,1
P056,2707848,2707848,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,G,1,G,1,1
P056,2769693,2769693,,C,T,GTA,ATA,Non-synonymous,Altering,SAR2682,SAR2682,putative aminotransferase,1,0,0,C,SNP,0,C,1,C,1,1
P056,1289651(self),NA,unknown,C,A,CTC,ATC,Non-synonymous,Altering,"(xbase, CDS NA)",(no ortholog),,1,0,0,C,SNP,0,NA,NA,C,1,1
P056,k31_var_137,2186517,,AG,A,GAT,ATA,"Frameshift, stop gained",Truncating,SAR2126,SAR2126,autoinducer sensor protein response regulator protein,0,1,0,D,ShINDEL,1,NA,NA,AG,1,1
P056,k31_var_160,NA,"2140135(M1, NC_021059.1)",T,TG,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,ShINDEL,1,NA,NA,T,1,1
P056,k31_var_63,886400,,T,TA,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,T,1,1
P056,k31_var_88,1249036,,C,CA,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,C,1,1
P056,k31_var_96,1555654,,AT,A,AAA,AAT,"Frameshift, stop gained",Truncating,SAR1463,SAR1463,endonuclease III,1,0,0,C,ShINDEL,1,NA,NA,AT,1,1
P057,20445,20445,,C,T,CGC,TGC,Non-synonymous,Altering,SAR0015,SAR0015,50S ribosomal protein L9,0,0,1,B,SNP,0,C,1,C,1,1
P057,556411,556411,,G,A,CGA,CAA,Non-synonymous,Altering,SAR0517,SAR0517,putative 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase,1,0,0,C,SNP,0,G,1,G,1,1
P057,675963,675963,,C,T,ATG,ATA,Non-synonymous,Altering,SAR0628,SAR0628,hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P057,1288032,1288032,,G,T,GCG,TCG,Non-synonymous,Altering,SAR1233,SAR1233,elongation factor Ts,1,0,0,C,SNP,0,G,1,G,1,1
P057,2136375,2136375,,G,T,GAC,GAA,Non-synonymous,Altering,SAR2048,SAR2048,hypothetical phage protein,1,0,0,C,SNP,0,G,1,NA,NA,1
P058,146858,146858,,G,A,GTG,GTA,Synonymous,Silent,SAR0133,SAR0133,putative membrane protein,1,0,0,C,SNP,0,G,1,G,1,1
P058,589266,589266,,C,T,GGC,GGT,Synonymous,Silent,SAR0544,SAR0544,50S ribosomal protein L10,1,0,0,C,SNP,0,C,1,C,1,1
P058,653537,653537,,T,C,TCT,CCT,Non-synonymous,Altering,SAR0602,SAR0602,putative membrane protein,0,0,1,B,SNP,0,T,1,T,1,1
P058,803790,803790,,G,T,GCA,TCA,Non-synonymous,Altering,SAR0771,SAR0771,conserved hypothetical protein,0,0,1,B,SNP,0,G,1,G,1,1
P058,887829,887829,,G,A,GGA,AGA,Non-synonymous,Altering,SAR0841,SAR0841,putative acetyltransferase,1,0,0,C,SNP,0,G,1,G,1,1
P058,1194188,1194188,,A,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P058,1459591,1459591,,G,A,ATC,ATT,Synonymous,Silent,SAR1402,SAR1402,phosphate-binding lipoprotein,0,0,1,B,SNP,0,G,1,G,1,1
P058,1471299,1471299,,C,A,GGC,GGA,Synonymous,Silent,SAR1412,SAR1412,diaminopimelate decarboxylase,1,0,0,C,SNP,0,C,1,C,1,1
P058,1607605,1607605,,T,C,ACA,GCA,Non-synonymous,Altering,SAR1508,SAR1508,hypothetical phage protein,1,0,0,C,SNP,0,T,1,NA,NA,1
P058,1792124,1792124,,T,A,AAA,TAA,Nonsense,Truncating,SAR1728,SAR1728,putative membrane protein,0,0,1,B,SNP,0,T,1,T,1,1
P058,1914056,1914056,,T,C,GTA,GCA,Non-synonymous,Altering,SAR1831,SAR1831,beta-lactamase precursor,0,0,1,B,SNP,0,T,1,NA,NA,1
P058,2448933,2448933,,G,A,ACT,ATT,Non-synonymous,Altering,SAR2382,SAR2382,putative transcriptional regulator,0,0,1,B,SNP,0,G,1,G,1,1
P058,2611161,2611161,,G,A,GCC,GTC,Non-synonymous,Altering,SAR2532,SAR2532,hypothetical protein,1,0,0,C,SNP,0,G,1,G,1,1
P058,2775648,2775648,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P058,1927215(self),NA,unknown,C,A,GGA,GTA,Non-synonymous,Altering,"(xbase, CDS NA)",(no ortholog),,0,1,0,D,SNP,0,NA,NA,NA,NA,NA
P058,k31_var_119,2855282,,CTTTA,C,ATT,AAT,"Frameshift, stop gained",Truncating,icaC,SAR2750,intercellular adhesion protein C,1,0,0,C,ShINDEL,4,NA,NA,NA,NA,NA
P059,380102,380102,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P059,545620,545620,,A,G,GCA,GCG,Synonymous,Silent,SAR0506,SAR0506,putative tetrapyrrole (corrin/porphyrin) methylases,1,0,0,C,SNP,0,A,1,A,1,1
P059,585494,585494,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,T,1,1
P059,609100,609100,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P059,689274,689274,,G,C,GCC,GCG,Synonymous,Silent,SAR0642,SAR0642,ABC transporter permease protein,1,0,0,C,SNP,0,G,1,G,1,1
P059,806244,806244,,C,T,GCA,GTA,Non-synonymous,Altering,SAR0772,SAR0772,putative sulfatase,1,0,0,C,SNP,0,C,1,C,1,1
P059,829289,829289,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P059,999766,999766,,T,G,CTC,CGC,Non-synonymous,Altering,SAR0954,SAR0954,transport system extracellular binding lipoprotein (pseudogene),0,1,0,D,SNP,0,T,1,T,1,1
P059,1223952,1223952,,G,C,GGA,GCA,Non-synonymous,Altering,SAR1177,SAR1177,putative dihydroorotase,1,0,0,C,SNP,0,G,1,G,1,1
P059,1454861,1454861,,T,C,ACT,ACC,Synonymous,Silent,SAR1397,SAR1397,putative peptidase,1,0,0,C,SNP,0,T,1,T,1,1
P059,1456796,1456796,,A,C,ATT,ATG,Non-synonymous,Altering,SAR1400,SAR1400,ABC transporter permease protein,1,0,0,C,SNP,0,A,1,A,1,1
P059,1463261,1463261,,A,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P059,1512181,1512181,,C,T,GCG,GCA,Synonymous,Silent,SAR1447,SAR1447,very large surface anchored protein,1,0,0,C,SNP,0,C,1,C,1,1
P059,1524139,1524139,,A,G,ATT,ATC,Synonymous,Silent,SAR1447,SAR1447,very large surface anchored protein,1,0,0,C,SNP,0,A,1,NA,NA,1
P059,1892120,1892120,,C,T,CAA,TAA,Nonsense,Truncating,SAR1813,SAR1813,histone deacetylase family protein,1,0,0,C,SNP,0,C,1,C,1,1
P059,1903201,1903201,,T,A,AAT,ATT,Non-synonymous,Altering,SAR1819,SAR1819,FtsK/SpoIIIE family protein,1,0,0,C,SNP,0,T,1,T,1,1
P059,1906306,1906306,,T,C,GCA,GCG,Synonymous,Silent,SAR1823,SAR1823,putative aminopeptidase,1,0,0,C,SNP,0,T,1,T,1,1
P059,2101039,2101039,,C,T,GGT,AGT,Non-synonymous,Altering,SAR2009,SAR2009,putative sodium:sulfate symporter,1,0,0,C,SNP,0,C,1,C,1,1
P059,2117836,2117836,,G,A,CAA,TAA,Nonsense,Truncating,SAR2027,SAR2027,putative membrane protein,1,0,0,C,SNP,0,G,1,G,1,1
P059,2320347,2320347,,G,A,ACT,ATT,Non-synonymous,Altering,SAR2248,SAR2248,putative surface anchored protein (pseudogene),1,0,0,C,SNP,0,G,1,G,1,1
P059,2418584,2418584,,C,T,CGT,CAT,Non-synonymous,Altering,SAR2345,SAR2345,AcrB/AcrD/AcrF family protein,1,0,0,C,SNP,0,C,1,C,1,1
P059,2474606,2474606,,C,T,ACG,ACA,Synonymous,Silent,SAR2405,SAR2405,sodium/bile acid symporter family protein (pseudogene),1,0,0,C,SNP,0,C,1,C,1,1
P059,2539924,2539924,,T,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P059,2668707,2668707,,T,C,ACA,ACG,Synonymous,Silent,SAR2585,SAR2585,MerR family regulatory protein,1,0,0,C,SNP,0,T,1,T,1,1
P059,2792706,2792706,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P059,2794452,2794452,,T,C,CCA,CCG,Synonymous,Silent,SAR2700,SAR2700,putative membrane protein,1,0,0,C,SNP,0,T,1,T,1,1
P059,1950561(self),2153665,,A,G,GAA,GAG,Synonymous,Silent,SAR2074,SAR2074,Similar to bacteriophage phi ETA hypothetical protein Orf32 ,1,0,0,C,SNP,0,NA,NA,A,1,1
P059,707560(self),754767,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,NA,NA,NA,NA,NA
P059,k31_var_200,2468789,,C,CT,TAC,ATA,"Frameshift, stop gained",Truncating,SAR2397,SAR2397,hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,C,1,1
P059,k31_var_34,1126014,,A,AT,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,AT,1,1
P059,k61_var_40,NA,"2140083(CA-347, NC_021554.1)",A,AT,TTA,TTT,"Frameshift, stop gained",Truncating,CA347_2111,SAR2125,accessory gene regulator protein C,1,0,0,C,ShINDEL,1,NA,NA,NA,NA,NA
P060,268892,268892,,C,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,0,NA,NA,0
P060,684040,684040,,G,A,CCG,CCA,Synonymous,Silent,SAR0637,SAR0637,sodium/hydrogen exchanger family protein,0,0,1,B,SNP,0,G,0,G,0,0
P060,880552,880552,,A,G,AAT,GAT,Non-synonymous,Altering,SAR0835,SAR0835,putative carboxylesterase,0,0,1,B,SNP,0,A,1,A,1,1
P060,1453857,1453857,,G,A,GAA,AAA,Non-synonymous,Altering,SAR1397,SAR1397,putative peptidase,0,0,1,B,SNP,0,G,0,G,0,0
P060,2511067,2511067,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P061,2841286,2841286,,C,T,GAT,AAT,Non-synonymous,Altering,SAR2734,SAR2734,serine-rich adhesin for platelets,0,1,0,D,SNP,0,C,1,C,1,1
P062,180114,180114,,T,C,TAC,CAC,Non-synonymous,Altering,SAR0161,SAR0161,capsular polysaccharide synthesis enzyme,0,0,1,B,SNP,0,C,0,T,0,0
P063,321283,321283,,C,A,CAG,CAT,Non-synonymous,Altering,SAR0276,SAR0276,putative membrane protein,0,1,0,D,SNP,0,C,1,C,1,1
P063,699479,699479,,T,G,TTC,TGC,Non-synonymous,Altering,SAR0653,SAR0653,ABC transporter ATP-binding protein,0,1,0,D,SNP,0,T,1,T,1,1
P063,947667,947667,,G,A,GCT,GTT,Non-synonymous,Altering,SAR0914,SAR0914,Na+/H+ antiporter subunit,0,0,1,B,SNP,0,G,0,G,0,0
P063,1022012,1022012,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,A,0,A,0,0
P063,1142554,1142554,,C,T,GGA,GAA,Non-synonymous,Altering,SAR1094,SAR1094,putative exported protein,0,1,0,D,SNP,0,C,1,C,1,1
P063,1192530,1192530,,T,C,ATA,ATG,Non-synonymous,Altering,SAR1147,SAR1147,putative membrane protein,0,1,0,D,SNP,0,T,0,T,0,0
P063,1337438,1337438,,A,G,CCA,CCG,Synonymous,Silent,SAR1272,SAR1272,DNA mismatch repair protein MutL,0,1,0,D,SNP,0,A,1,NA,NA,1
P063,1677070,1677070,,A,G,ATT,ATC,Synonymous,Silent,SAR1604,SAR1604,biotin carboxylase subunit of acetyl-CoA carboxylase,0,1,0,D,SNP,0,A,0,A,0,0
P063,1737530,1737530,,C,T,GGC,AGC,Non-synonymous,Altering,SAR1669,SAR1669,conserved hypothetical protein,0,1,0,D,SNP,0,C,1,C,1,1
P063,1917985,1917985,,A,T,ATT,AAT,Non-synonymous,Altering,SAR1835,SAR1835,putative D-alanine aminotransferase,0,1,0,D,SNP,0,A,0,A,0,0
P063,1927323,1927323,,T,C,ACC,GCC,Non-synonymous,Altering,SAR1841,SAR1841,putative surface anchored protein,0,1,0,D,SNP,0,T,0,T,0,0
P063,2044063,2044063,,G,A,CCA,CTA,Non-synonymous,Altering,SAR1953,SAR1953,AhpC/TSA family protein,0,1,0,D,SNP,0,G,0,G,0,0
P063,2300741,2300741,,T,C,CCA,CCG,Synonymous,Silent,SAR2232,SAR2232,conserved hypothetical protein,0,1,0,D,SNP,0,T,0,T,0,0
P063,2339220,2339220,,G,A,GGC,GGT,Synonymous,Silent,SAR2257,SAR2257,putative transport protein (pseudogene),0,1,0,D,SNP,0,G,0,G,0,0
P063,2456091,2456091,,A,C,ACA,ACC,Synonymous,Silent,SAR2388,SAR2388,putative exported protein,0,1,0,D,SNP,0,A,0,A,0,0
P063,2535520,2535520,,G,A,GGA,AGA,Non-synonymous,Altering,SAR2464,SAR2464,TetR family regulatory protein,0,1,0,D,SNP,0,G,0,G,0,0
P063,2804147,2804147,,G,A,GCT,GTT,Non-synonymous,Altering,SAR2709,SAR2709,clumping factor B,0,1,0,D,SNP,0,G,0,G,0,0
P063,1893267(self),NA,unknown,C,T,ACA,ATA,Non-synonymous,Altering,"(RAST, CDS NA)",(no ortholog),hypothetical protein,0,1,0,D,SNP,0,NA,NA,C,1,1
P063,2465630(self),NA,"2554344(MSSA476, BX571857.1)",G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,NA,NA,A,0,0
P063,k31_var_170,2350398,,C,CT,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,ShINDEL,1,NA,NA,C,1,1
P063,k31_var_176,NA,"2554866(MSSA476, BX571857.1)",AT,A,ATA,TAC,"Frameshift, stop gained",Truncating,SAS2385,(no ortholog),putative staphylococcal accessory regulator,0,1,0,D,ShINDEL,1,NA,NA,AT,1,1
P063,k31_var_200,429544,,TT,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,ShINDEL,1,NA,NA,TT,1,1
P063,k61_var_158,2068449,,T,TTTCTCTATGTTGGGGCCCCGCCAACCTGCACATTATCGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGCCCACACCCCAACTTGCATTGCCTGTAGAATTTCTTTTTTGAAA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,ShINDEL,115,NA,NA,TTTCTCTATGTTGGGGCCCCGCCAACCTGCACATTATCGTAAGCTGACTTTTCGTCAGCTTCTGTGTTGGGGCCCACACCCCAACTTGCATTGCCTGTAGAATTTCTTTTTTGAAA,0,0
P064,2233917,2233917,,C,T,GGC,GAC,Non-synonymous,Altering,SAR2165,SAR2165,putative potassium-transporting ATPase a chain,1,0,0,C,SNP,0,C,1,C,1,1
P064,2783243,2783243,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,1,A,1,1
P064,794528(self),919105,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,NA,NA,NA
P064,k31_var_111,2093565,,TC,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,TC,1,1
P064,k31_var_210,2845630,,G,A,TAC,TGC,Non-synonymous,Altering,SAR2738,SAR2738,hypothetical protein,0,0,1,B,SNP,0,NA,NA,A,0,0
P064,k31_var_219,NA,"104534(CA-347, NC_021554.1)",T,C,GGA,GGG,Synonymous,Silent,CA347_95,(no ortholog),N-acetyl-ornithine/N-acetyl-lysine deacetylase family protein,0,0,1,B,SNP,0,NA,NA,T,1,1
P064,k61_var_90,2843436,,AT,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,AT,1,1
P065,361381,361381,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P065,1483687,1483687,,G,T,CCT,CAT,Non-synonymous,Altering,SAR1425,SAR1425,2-oxoglutarate dehydrogenase E1 component,1,0,0,C,SNP,0,G,1,G,1,1
P065,1842227,1842227,,G,A,TCA,TTA,Non-synonymous,Altering,SAR1774,SAR1774,citrate synthase II,1,0,0,C,SNP,0,G,1,G,1,1
P065,1842468,1842468,,G,T,CAG,AAG,Non-synonymous,Altering,SAR1774,SAR1774,citrate synthase II,1,0,0,C,SNP,0,G,1,G,1,1
P065,1842563,1842563,,G,A,ACA,ATA,Non-synonymous,Altering,SAR1774,SAR1774,citrate synthase II,1,0,0,C,SNP,0,G,1,G,1,1
P065,2499286,2499286,,A,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P065,k31_var_168,2223082,,TC,T,CAA,AAA,"Frameshift, stop gained",Truncating,sigB,SAR2152,"RNA polymerase sigma factor SigB (sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma B is not essential for sporulation; rather it is required for maximal expression of ctc and csbA which are transcribed in the early stationary phase under conditions inimical to sporulation; induced by heat shock, salt stress, oxidative stress, glucose limitation, oxygen limitation and entry into stationary phase)",1,0,0,C,ShINDEL,1,NA,NA,TC,1,1
P066,1552820,1552820,,T,A,GTT,GAT,Non-synonymous,Altering,SAR1461,SAR1461,penicillin-binding protein 2,0,0,1,B,SNP,0,T,0,T,0,0
P066,2434211,2434211,,T,C,GGT,GGC,Synonymous,Silent,SAR2364,SAR2364,FdhD/NarQ family protein,1,0,0,C,SNP,0,T,1,T,1,1
P066,2490726,2490726,,A,T,CAT,CTT,Non-synonymous,Altering,SAR2421,SAR2421,putative membrane protein,1,0,0,C,SNP,0,A,1,NA,NA,1
P066,2618493,2618493,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P067,405343,405343,,G,A,ATG,ATA,Non-synonymous,Altering,SAR0358,SAR0358,putative membrane protein,1,0,0,C,SNP,0,G,1,G,1,1
P067,1074917,1074917,,G,T,CCT,ACT,Non-synonymous,Altering,SAR1029,SAR1029,putative exported protein,1,0,0,C,SNP,0,G,1,G,1,1
P067,1270681,1270681,,T,G,TCA,TCC,Synonymous,Silent,SAR1218,SAR1218,putative membrane protein,0,1,0,D,SNP,0,T,NA,NA,NA,NA
P067,1757105,1757105,,G,A,CCA,TCA,Non-synonymous,Altering,SAR1697,SAR1697,putative alanyl-tRNA synthetase,1,0,0,C,SNP,0,G,1,G,1,1
P067,2276382,2276382,,G,A,CCT,TCT,Non-synonymous,Altering,SAR2209,SAR2209,transcription termination factor,0,1,0,D,SNP,0,G,NA,G,1,1
P067,1389293(self),2130148,,C,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,NA,NA,NA,NA,NA
P068,718667,718667,,G,A,AGC,AAC,Non-synonymous,Altering,SAR0672,SAR0672,putative ABC transporter permease,0,0,1,B,SNP,0,G,0,G,0,0
P068,952932,952932,,C,A,TTC,TTA,Non-synonymous,Altering,SAR0918,SAR0918,NADH:flavin oxidoreductase / NADH oxidase family protein,0,1,0,D,SNP,0,C,1,C,1,1
P068,1091306,1091306,,G,T,GAT,TAT,Non-synonymous,Altering,SAR1045,SAR1045,putative phosphoribosylformylglycinamidine cyclo-ligase,1,0,0,C,SNP,0,G,1,G,1,1
P068,1802244,1802244,,C,A,GCT,TCT,Non-synonymous,Altering,SAR1733,SAR1733,DNA repair protein RadC (pseudogene),0,1,0,D,SNP,0,C,1,C,1,1
P068,2110840,2110840,,C,A,GCG,GAG,Non-synonymous,Altering,SAR2017,SAR2017,hypothetical protein,0,1,0,D,SNP,0,C,1,C,1,1
P068,2613582,2613582,,G,T,TCA,TAA,Nonsense,Truncating,SAR2534,SAR2534,putative transport protein,0,1,0,D,SNP,0,G,1,G,1,1
P069,6767,6767,,A,G,GCA,GCG,Synonymous,Silent,SAR0005,SAR0005,DNA gyrase subunit B,1,0,0,C,SNP,0,G,1,G,1,1
P069,710480,710480,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P069,1552471,1552471,,C,T,CGT,TGT,Non-synonymous,Altering,SAR1461,SAR1461,penicillin-binding protein 2,1,0,0,C,SNP,0,C,1,C,1,1
P069,1552504,1552504,,C,A,CGT,AGT,Non-synonymous,Altering,SAR1461,SAR1461,penicillin-binding protein 2,1,0,0,C,SNP,0,C,1,C,1,1
P069,1552867,1552867,,C,T,CGT,TGT,Non-synonymous,Altering,SAR1461,SAR1461,penicillin-binding protein 2,1,0,0,C,SNP,0,C,1,C,1,1
P069,1938497,1938497,,A,T,CTT,CAT,Non-synonymous,Altering,SAR1848,SAR1848,conserved hypothetical protein,1,0,0,C,SNP,0,A,1,A,1,1
P069,2705974(self),NA,"394117(MSSA476, BX571857.1)",C,T,TTC,TTT,Synonymous,Silent,SAS0347,(no ortholog),toxin,1,0,0,C,SNP,0,NA,NA,C,1,1
P070,1554504,1554504,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,1,C,1,1
P070,2351356,2351356,,A,G,ATT,ATC,Synonymous,Silent,SAR2269,SAR2269,hypothetical protein,0,0,1,B,SNP,0,A,1,A,1,1
P070,k31_var_255,NA,"457308(Newman, AP009351.1)",A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,A,1,1
P071,552599,552599,,A,G,ACA,ACG,Synonymous,Silent,SAR0513,SAR0513,putative chaperonin,0,0,1,B,SNP,0,A,1,A,1,1
P071,630770,630770,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,1,C,1,1
P071,861990,861990,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,1,C,1,1
P071,1174397,1174397,,T,C,TGT,TGC,Synonymous,Silent,SAR1125,SAR1125,conserved hypothetical protein,0,0,1,B,SNP,0,T,1,T,1,1
P071,2382439,2382439,,C,T,GTT,ATT,Non-synonymous,Altering,SAR2297,SAR2297,putative acetolactate synthase,0,0,1,B,SNP,0,C,0,C,0,0
P072,110018,110018,,G,T,GAA,TAA,Nonsense,Truncating,SAR0105,SAR0105,1-phosphatidylinositol phosphodiesterase,0,1,0,D,SNP,0,G,1,G,1,1
P072,273746,273746,,A,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,T,1,T,1,1
P072,275139,275139,,T,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P072,346621,346621,,C,A,CAA,AAA,Non-synonymous,Altering,SAR0304,SAR0304,putative exported protein,0,1,0,D,SNP,0,C,1,C,1,1
P072,376168,376168,,G,A,GCA,ACA,Non-synonymous,Altering,SAR0330,SAR0330,MarR family regulatory protein,0,1,0,D,SNP,0,G,1,G,1,1
P072,384890,384890,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,C,1,NA,NA,1
P072,489278,489278,,C,T,CCT,CTT,Non-synonymous,Altering,SAR0460,SAR0460,putative Cys/Met metabolism PLP-dependent enzyme,0,0,1,B,SNP,0,C,0,C,0,0
P072,533662,533662,,T,C,AAT,AAC,Synonymous,Silent,SAR0496,SAR0496,conserved hypothetical protein,0,1,0,D,SNP,0,T,0,T,0,0
P072,582620,582620,,C,T,CCC,TCC,Non-synonymous,Altering,SAR0533,SAR0533,cysteinyl-tRNA synthetase,0,1,0,D,SNP,0,C,1,C,1,1
P072,745220,745220,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,C,1,C,1,1
P072,837862,837862,,C,G,GGT,GCT,Non-synonymous,Altering,SAR0800,SAR0800,putative membrane protein,0,1,0,D,SNP,0,C,1,C,1,1
P072,860160,860160,,T,C,AGT,AGC,Synonymous,Silent,SAR0817,SAR0817,conserved hypothetical protein,0,1,0,D,SNP,0,T,1,T,1,1
P072,866138,866138,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,C,1,C,1,1
P072,1152404,1152404,,G,T,GGC,TGC,Non-synonymous,Altering,SAR1106,SAR1106,putative transport system extracellular binding lipoprotein,0,0,1,B,SNP,0,G,0,G,0,0
P072,1226832,1226832,,C,T,GCC,GCT,Synonymous,Silent,SAR1179,SAR1179,"putative carbamoyl-phosphate synthase, pyrimidine-specific, large chain",1,0,0,C,SNP,0,C,1,C,1,1
P072,1320747,1320747,,C,T,CCA,CTA,Non-synonymous,Altering,SAR1259,SAR1259,putative CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase,0,1,0,D,SNP,0,C,1,C,1,1
P072,1412529,1412529,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,T,1,T,1,1
P072,1451691,1451691,,A,G,GGT,GGC,Synonymous,Silent,SAR1395,SAR1395,putative oligopeptide transport system permease,0,1,0,D,SNP,0,G,1,G,1,1
P072,1506130,1506130,,A,G,AAT,AAC,Synonymous,Silent,SAR1447,SAR1447,very large surface anchored protein,0,1,0,D,SNP,0,A,1,A,1,1
P072,1577934,1577934,,G,T,GCT,GAT,Non-synonymous,Altering,SAR1484,SAR1484,putative GTPase,1,0,0,C,SNP,0,G,1,G,1,1
P072,1620227,1620227,,G,A,CGT,TGT,Non-synonymous,Altering,SAR1525,SAR1525,hypothetical phage protein,1,0,0,C,SNP,0,G,1,G,1,1
P072,1697551,1697551,,A,G,AGT,AGC,Synonymous,Silent,SAR1629,SAR1629,penicillin-binding protein PBP2B,0,1,0,D,SNP,0,A,1,A,1,1
P072,1852775,1852775,,C,T,GAA,AAA,Non-synonymous,Altering,SAR1781,SAR1781,DNA polymerase III alpha subunit,0,1,0,D,SNP,0,C,1,C,1,1
P072,2066899,2066899,,A,C,CAT,CAG,Non-synonymous,Altering,SAR1977,SAR1977,hypothetical protein,0,1,0,D,SNP,0,A,0,A,0,0
P072,2224203,2224203,,T,C,GAT,GGT,Non-synonymous,Altering,SAR2154,SAR2154,anti-sigma B factor antagonist,0,1,0,D,SNP,0,T,1,T,1,1
P072,2412199,2412199,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P072,2814074,2814074,,T,C,TAT,TGT,Non-synonymous,Altering,SAR2717,SAR2717,immunodominant antigen B,0,1,0,D,SNP,0,T,1,T,1,1
P072,2848342,2848342,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,C,1,C,1,1
P072,1058440(self),1624399,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,NA,NA,C,1,1
P072,2506569(self),NA,"208018(MSSA476, BX571857.1)",G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,NA,NA,NA,NA,NA
P072,2616440(self),NA,"318164(MSSA476, BX571857.1)",A,C,GAT,GCT,Non-synonymous,Altering,SAS0269,SAR0293,hypothetical protein,0,1,0,D,SNP,0,NA,NA,A,1,1
P072,k31_var_104,504629,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,NA,NA,A,1,1
P072,k31_var_46,NA,"62624(CN1, NC_022226.1)",C,CA,AAT,AAA,"Frameshift, stop gained",Truncating,SAS0178,(no ortholog),ABC transporter ATP-binding protein,0,1,0,D,ShINDEL,1,NA,NA,CA,0,0
P072,k31_var_52,1616040,,G,GG,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,ShINDEL,1,NA,NA,G,1,1
P072,k31_var_77,NA,"1893647(MSSA476, BX571857.1)",GT,G,ACT,CTT,"Frameshift, stop gained",Truncating,SAS1745,(no ortholog),hypothetical protein,0,1,0,D,ShINDEL,1,NA,NA,GT,1,1
P072,k61_var_30,NA,"596981(MSSA476, BX571857.1)",A,ATAGCGATTCAGACTCAGA,GAC,GAT,"Non-synonymous, 6 codon insertion",Altering,SAS0519,SAR0566,serine-aspartate repeat-containing protein C,0,1,0,D,ShINDEL,18,NA,NA,ATAGCGATTCAGACTCAGA,0,0
P073,157422,157422,,G,A,TCA,TTA,Non-synonymous,Altering,SAR0143,SAR0143,binding-protein-dependent transport system membrane component,0,0,1,B,SNP,0,G,1,G,1,1
P073,252651,252651,,G,A,GTA,ATA,Non-synonymous,Altering,SAR0217,SAR0217,formate acetyltransferase,0,0,1,B,SNP,0,G,1,G,1,1
P073,550924,550924,,G,A,GGT,AGT,Non-synonymous,Altering,SAR0512,SAR0512,putative cell division protein,0,0,1,B,SNP,0,G,0,G,0,0
P073,570741,570741,,G,A,GCC,GCT,Synonymous,Silent,SAR0524,SAR0524,nucleoside permease,0,0,1,B,SNP,0,G,0,G,0,0
P073,584780,584780,,G,T,CGT,CTT,Non-synonymous,Altering,SAR0535,SAR0535,SpoU rRNA Methylase family protein,0,0,1,B,SNP,0,G,0,G,0,0
P073,640860,640860,,G,T,AGA,ATA,Non-synonymous,Altering,SAR0589,SAR0589,putative amino acid permease,0,0,1,B,SNP,0,G,0,G,0,0
P073,651869,651869,,A,G,GGT,GGC,Synonymous,Silent,SAR0600,SAR0600,pyridine nucleotide-disulphide oxidoreductase protein,0,0,1,B,SNP,0,G,0,G,0,0
P073,663916,663916,,G,T,GCT,TCT,Non-synonymous,Altering,SAR0615,SAR0615,putative arginyl-tRNA synthetase,1,0,0,C,SNP,0,G,1,G,1,1
P073,668960,668960,,A,G,TAC,TGC,Non-synonymous,Altering,SAR0620,SAR0620,haloacid dehalogenase-like hydrolase,0,0,1,B,SNP,0,A,0,A,0,0
P073,719559,719559,,G,A,ATG,ATA,Non-synonymous,Altering,SAR0672,SAR0672,ABC transporter permease,0,0,1,B,SNP,0,G,1,G,1,1
P073,820246,820246,,A,G,GCT,GCC,Synonymous,Silent,SAR0783,SAR0783,putative membrane protein,0,0,1,B,SNP,0,A,0,A,0,0
P073,934764,934764,,T,G,GCA,GCC,Synonymous,Silent,SAR0898,SAR0898,conserved hypothetical protein,0,0,1,B,SNP,0,T,0,T,0,0
P073,1087104,1087104,,A,G,TAT,TGT,Non-synonymous,Altering,SAR1043,SAR1043,putative phosphoribosylformylglycinamidine synthase II,0,0,1,B,SNP,0,A,0,A,0,0
P073,1089030,1089030,,C,T,GCA,GTA,Non-synonymous,Altering,SAR1043,SAR1043,putative phosphoribosylformylglycinamidine synthase II,0,0,1,B,SNP,0,C,0,C,0,0
P073,1100869,1100869,,A,G,CAA,CGA,Non-synonymous,Altering,SAR1054,SAR1054,conserved hypothetical protein,0,0,1,B,SNP,0,A,0,A,0,0
P073,1113945,1113945,,A,G,ATG,GTG,Non-synonymous,Altering,SAR1067,SAR1067,"putative pyruvate dehydrogenase E1 component, alpha subunit",1,0,0,C,SNP,0,A,1,A,1,1
P073,1160775,1160775,,T,C,ACC,GCC,Non-synonymous,Altering,SAR1113,SAR1113,putative ribonuclease,1,0,0,C,SNP,0,T,1,T,1,1
P073,1214628,1214628,,C,T,CCT,TCT,Non-synonymous,Altering,SAR1169,SAR1169,isoleucyl-tRNA synthetase,0,0,1,B,SNP,0,C,0,C,0,0
P073,1224556,1224556,,A,G,CAA,CGA,Non-synonymous,Altering,SAR1178,SAR1178,"putative carbamoyl-phosphate synthase, pyrimidine-specific, small chain",0,0,1,B,SNP,0,A,0,A,0,0
P073,1251401,1251401,,C,T,GCA,GTA,Non-synonymous,Altering,SAR1202,SAR1202,conserved hypothetical protei,1,0,0,C,SNP,0,C,1,C,1,1
P073,1338463,1338463,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,0,C,0,0
P073,1512050,1512050,,C,T,GGT,GAT,Non-synonymous,Altering,SAR1447,SAR1447,very large surface anchored protein,0,0,1,B,SNP,0,C,0,C,0,0
P073,1550226,1550226,,C,T,TCG,TCA,Synonymous,Silent,SAR1458,SAR1458,conserved hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P073,1732825,1732825,,G,A,CCA,CTA,Non-synonymous,Altering,SAR1664,SAR1664,conserved hypothetical protein,0,0,1,B,SNP,0,G,0,G,0,0
P073,1766688,1766688,,T,C,CGT,CGC,Synonymous,Silent,SAR1703,SAR1703,putative oxygenase,0,0,1,B,SNP,0,T,0,T,0,0
P073,1887207,1887207,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,0,T,0,0
P073,2074676,2074676,,T,C,ACA,GCA,Non-synonymous,Altering,SAR1986,SAR1986,ImpB/MucB/SamB family protein,0,0,1,B,SNP,0,T,0,T,0,0
P073,2097725,2097725,,T,C,GAT,GGT,Non-synonymous,Altering,SAR2006,SAR2006,conserved hypothetical protein,0,0,1,B,SNP,0,T,0,T,0,0
P073,2125511,2125511,,T,C,GCT,GCC,Synonymous,Silent,SAR2034,SAR2034,putative membrane protein,0,0,1,B,SNP,0,T,0,T,0,0
P073,2145841,2145841,,T,C,GAT,GGT,Non-synonymous,Altering,SAR2061,SAR2061,hypothetical phage protein,0,0,1,B,SNP,0,T,0,NA,NA,0
P073,2272437,2272437,,T,C,GAT,GGT,Non-synonymous,Altering,SAR2205,SAR2205,conserved hypothetical protein,1,0,0,C,SNP,0,T,1,T,1,1
P073,2428614,2428614,,G,T,CCT,ACT,Non-synonymous,Altering,SAR2357,SAR2357,putative molybdenum cofactor biosynthesis protein,1,0,0,C,SNP,0,G,1,G,1,1
P073,2492621,2492621,,G,T,AAG,AAT,Non-synonymous,Altering,SAR2423,SAR2423,conserved hypothetical protein,0,0,1,B,SNP,0,G,0,G,0,0
P073,2597831,2597831,,C,T,ACC,ACT,Synonymous,Silent,SAR2522,SAR2522,putative glycerate kinase,0,0,1,B,SNP,0,C,0,C,0,0
P073,2738869,2738869,,C,T,GGG,AGG,Non-synonymous,Altering,SAR2649,SAR2649,O-acetyltransferase OatA,0,0,1,B,SNP,0,C,1,C,1,1
P073,2746475,2746475,,C,T,CAA,TAA,Nonsense,Truncating,SAR2658,SAR2658,TetR family regulatory protein,0,0,1,B,SNP,0,C,1,C,1,1
P073,1258343(self),1372289,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,T,1,1
P073,k31_var_12,1483148,,C,CA,GAT,TGA,Nonsense,Truncating,SAR1425,SAR1425,2-oxoglutarate dehydrogenase E1 component,0,0,1,B,ShINDEL,1,NA,NA,C,1,1
P073,k31_var_23,1397692,,T,TA,ATG,AAT,"Frameshift, stop gained",Truncating,SAR1347,SAR1347,GMP reductase,0,0,1,B,ShINDEL,1,NA,NA,TA,0,0
P073,k31_var_27,796596,,G,GG,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,G,1,1
P073,k31_var_29,125504,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,NA,NA,G,1,1
P073,k31_var_33,2183916,,GT,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,G,0,0
P073,k31_var_50,NA,"2073289(MSSA476, BX571857.1)",CT,C,AGG,GGT,"Frameshift, stop gained",Truncating,SAS1927,(no ortholog),hypothetical protein,0,0,1,B,ShINDEL,1,NA,NA,C,0,0
P073,k31_var_61,2562632,,CAT,C,ATA,ATG,Frameshift with readthrough,Altering,SAR2488,SAR2488,nitrite reductase NAD(P)H small subunit,0,0,1,B,ShINDEL,2,NA,NA,C,0,0
P073,k31_var_74,620069,,C,CA,ACA,CAC,"Frameshift, stop gained",Truncating,SAR0567,SAR0567,bone sialoprotein-binding protein,0,0,1,B,ShINDEL,1,NA,NA,CA,0,0
P073,k31_var_77,2186558,,A,AA,AAT,ATT,"Frameshift, stop gained",Truncating,SAR2126,SAR2126,autoinducer sensor protein response regulator protein,0,0,1,B,ShINDEL,1,NA,NA,AA,0,0
P073,k61_var_13,2531229,,AT,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,A,0,0
P073,k61_var_38,576701,,T,TA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,TA,0,0
P073,k61_var_49,1880853,,TT,T,AAA,AAG,"Frameshift, stop gained",Truncating,SAR1805,SAR1805,serine protease,1,0,0,C,ShINDEL,1,NA,NA,TT,1,1
P073,k61_var_73,1654056,,C,CT,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,CT,0,0
P074,1825644,1825644,,T,C,CCA,CCG,Synonymous,Silent,SAR1762,SAR1762,threonyl-tRNA synthetase,0,0,1,B,SNP,0,T,1,T,1,1
P075,2237626,2237626,,C,T,GCT,GTT,Non-synonymous,Altering,SAR2166,SAR2166,sensor kinase protein,1,0,0,C,SNP,0,C,1,C,1,1
P076,899443,899443,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,0,T,0,0
P076,1177564,1177564,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,T,1,T,1,1
P076,1206364,1206364,,A,T,ATT,TTT,Non-synonymous,Altering,SAR1161,SAR1161,putative cell division protein,0,0,1,B,SNP,0,A,1,A,1,1
P076,1535341,1535341,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,0,C,0,0
P076,1689995,1689995,,C,G,GGT,GCT,Non-synonymous,Altering,SAR1620,SAR1620,putative membrane protein,0,0,1,B,SNP,0,C,0,C,0,0
P076,2224554,2224554,,G,T,CAC,CAA,Non-synonymous,Altering,SAR2155,SAR2155,putative sigma factor sigB regulation protein,0,0,1,B,SNP,0,G,1,G,1,1
P076,2043358(self),NA,"2555103(MSSA476, BX571857.1)",G,A,AGG,AGA,Synonymous,Silent,SAS2385,(no ortholog),putative staphylococcal accessory regulator,0,0,1,B,SNP,0,NA,NA,G,0,0
P076,359276(self),NA,unknown,G,T,TGA,TTA,Nonsense,Truncating,unknown,(no ortholog),Phage minor structural protein homology to YP_001004386.1 on Staphylococcus phage phiETA3,0,0,1,B,SNP,0,NA,NA,G,1,1
P076,k31_var_80,2070381,,CA,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,C,0,0
P077,228554,228554,,A,T,TTT,TTA,Non-synonymous,Altering,SAR0198,SAR0198,ABC transporter ATP-binding protein,0,0,1,B,SNP,0,A,1,A,1,1
P077,349251,349251,,C,T,CAA,TAA,Nonsense,Truncating,SAR0306,SAR0306,ABC transporter ATP-binding protein,0,0,1,B,SNP,0,C,1,NA,NA,1
P077,609124,609124,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,1,NA,NA,1
P077,614336,614336,,G,A,TGT,TAT,Non-synonymous,Altering,SAR0563,SAR0563,putative deaminase,0,0,1,B,SNP,0,G,0,G,0,0
P077,683876,683876,,C,A,CCT,ACT,Non-synonymous,Altering,SAR0637,SAR0637,sodium/hydrogen exchanger family protein,0,0,1,B,SNP,0,C,0,C,0,0
P077,791692,791692,,G,A,GAT,AAT,Non-synonymous,Altering,SAR0755,SAR0755,putative membrane protein,0,0,1,B,SNP,0,G,0,NA,NA,0
P077,851007,851007,,A,G,TTA,TTG,Synonymous,Silent,SAR0810,SAR0810,putative phosphohydrolase,0,0,1,B,SNP,0,A,1,A,1,1
P077,851334,851334,,A,G,ATT,GTT,Non-synonymous,Altering,SAR0811,SAR0811,putative membrane protein,0,0,1,B,SNP,0,A,0,A,0,0
P077,1023367,1023367,,C,A,GCA,TCA,Non-synonymous,Altering,SAR0979,SAR0979,putative membrane protein,0,0,1,B,SNP,0,C,0,C,0,0
P077,1056194,1056194,,T,C,TCA,CCA,Non-synonymous,Altering,SAR1014,SAR1014,acetyltransferase (GNAT) family protein,0,0,1,B,SNP,0,T,1,NA,NA,1
P077,1064069,1064069,,G,A,AAC,AAT,Synonymous,Silent,SAR1022,SAR1022,glutamyl endopeptidase precursor,0,0,1,B,SNP,0,G,1,NA,NA,1
P077,1127458,1127458,,G,C,GTT,CTT,Non-synonymous,Altering,SAR1081,SAR1081,inositol monophosphatase family protein,0,0,1,B,SNP,0,G,0,NA,NA,0
P077,1144237,1144237,,A,G,ACG,GCG,Non-synonymous,Altering,SAR1098,SAR1098,putative phosphopantetheine adenylyltransferase,0,0,1,B,SNP,0,A,0,A,0,0
P077,1179907,1179907,,T,C,ATT,GTT,Non-synonymous,Altering,SAR1134,SAR1134,hypothetical protein,0,0,1,B,SNP,0,T,1,NA,NA,1
P077,1298747,1298747,,G,A,GAT,AAT,Non-synonymous,Altering,SAR1240,SAR1240,DNA polymerase III PolC-type,0,0,1,B,SNP,0,G,0,NA,NA,0
P077,1317400,1317400,,C,T,CGT,TGT,Non-synonymous,Altering,SAR1255,SAR1255,putative protease,0,0,1,B,SNP,0,C,0,NA,NA,0
P077,1420848,1420848,,G,A,AAG,AAA,Synonymous,Silent,SAR1367,SAR1367,topoisomerase IV subunit A,0,0,1,B,SNP,0,G,0,NA,NA,0
P077,1479381,1479381,,T,C,TTA,TTG,Synonymous,Silent,SAR1421,SAR1421,conserved hypothetical protein,0,0,1,B,SNP,0,T,1,NA,NA,1
P077,1584463,1584463,,G,A,CCA,TCA,Non-synonymous,Altering,SAR1489,SAR1489,cell surface elastin binding protein,1,0,0,C,SNP,0,G,1,G,1,1
P077,1651371,1651371,,C,T,TTG,TTA,Synonymous,Silent,SAR1581,SAR1581,conserved hypothetical protein,0,0,1,B,SNP,0,C,0,C,0,0
P077,1831955,1831955,,G,A,CAC,TAC,Non-synonymous,Altering,SAR1768,SAR1768,formamidopyrimidine-DNA glycosylase,0,0,1,B,SNP,0,G,1,NA,NA,1
P077,1874461,1874461,,A,G,AAT,AGT,Non-synonymous,Altering,SAR1800,SAR1800,putative soluble hydrogenase subunit,0,0,1,B,SNP,0,A,0,NA,NA,0
P077,1917656,1917656,,C,T,GCT,ACT,Non-synonymous,Altering,SAR1835,SAR1835,putative D-alanine aminotransferase,1,0,0,C,SNP,0,C,1,C,1,1
P077,2081442,2081442,,T,C,TCA,TCG,Synonymous,Silent,SAR1992,SAR1992,glutamyl-tRNA amidotransferase subunit A,0,0,1,B,SNP,0,T,0,T,0,0
P077,2083069,2083069,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,0,NA,NA,0
P077,2173199,2173199,,C,T,GCC,GTC,Non-synonymous,Altering,SAR2109,SAR2109, succinyl-diaminopimelate desuccinylase,1,0,0,C,SNP,0,C,1,C,1,1
P077,2173488,2173488,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,1,NA,NA,1
P077,2186692,2186692,,C,T,CGT,TGT,Non-synonymous,Altering,SAR2126,SAR2126,autoinducer sensor protein response regulator protein,0,0,1,B,SNP,0,C,1,NA,NA,1
P077,2189764,2189764,,A,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P077,2198623,2198623,,T,C,TTT,TTC,Synonymous,Silent,SAR2135,SAR2135,putative membrane protein,0,0,1,B,SNP,0,T,0,T,0,0
P077,2205487,2205487,,C,A,CGC,AGC,Non-synonymous,Altering,SAR2141,SAR2141,acetolactate synthase large subunit,1,0,0,C,SNP,0,A,1,A,1,1
P077,2294356,2294356,,A,T,AAT,ATT,Non-synonymous,Altering,SAR2226,SAR2226,putative purine nucleoside phosphorylase,0,0,1,B,SNP,0,A,0,NA,NA,0
P077,2412294,2412294,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,0,A,0,0
P077,2473308,2473308,,A,G,GTT,GCT,Non-synonymous,Altering,SAR2403,SAR2403,putative membrane protein,0,0,1,B,SNP,0,A,1,A,1,1
P077,2489943,2489943,,G,A,CCA,TCA,Non-synonymous,Altering,SAR2420,SAR2420,arginase family protein,0,0,1,B,SNP,0,G,1,NA,NA,1
P077,2497405,2497405,,G,A,ACA,ATA,Non-synonymous,Altering,SAR2428,SAR2428,putative membrane protein,0,0,1,B,SNP,0,G,0,NA,NA,0
P077,2498554,2498554,,T,C,GCT,GCC,Synonymous,Silent,SAR2429,SAR2429,putative 3-methylpurine glycosylase,0,0,1,B,SNP,0,T,1,NA,NA,1
P077,2574651,2574651,,T,C,AAT,GAT,Non-synonymous,Altering,SAR2502,SAR2502,ABC transporter ATP-binding protein,0,0,1,B,SNP,0,T,0,NA,NA,0
P077,2791528,2791528,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,0,NA,NA,0
P077,k31_var_13,NA,"434139(RF122, NC_007622.1)",T,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,T,1,1
P077,k31_var_15,608833,,GA,G,GAA,GAA,"Frameshift, stop gained",Truncating,SAR0557,SAR0557,ribulokinase,1,0,0,C,ShINDEL,1,NA,NA,GA,1,1
P077,k31_var_17004,907722,,AA,A,AGG,GGG,"Frameshift, stop gained",Truncating,SAR0867,SAR0867,topiosmerase,0,0,1,B,ShINDEL,1,NA,NA,AA,1,1
P077,k31_var_17032,2126006,,CTAGCTTGTGC,C,AGC,CAC,"Frameshift, stop gained",Truncating,SAR2035,SAR2035,hypothetical protein,0,0,1,B,ShINDEL,10,NA,NA,CTAGCTTGTGC,1,1
P077,k31_var_86,1905333,,A,AT,GGA,TGG,"Frameshift, stop gained",Truncating,SAR1822,SAR1822,thioredoxin,1,0,0,C,ShINDEL,1,NA,NA,A,1,1
P078,880492,880492,,C,A,CTT,ATT,Non-synonymous,Altering,SAR0835,SAR0835,putative carboxylesterase,1,0,0,C,SNP,0,C,1,C,1,1
P078,1537529,1537529,,A,G,TCT,TCC,Synonymous,Silent,SAR1449,SAR1449,amino acid permease,1,0,0,C,SNP,0,A,1,A,1,1
P078,1930859,1930859,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P079,902360,902360,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P079,958535,958535,,G,A,ACA,ATA,Non-synonymous,Altering,SAR0922,SAR0922,putative argininosuccinate lyase,0,0,1,B,SNP,0,G,1,G,1,1
P079,1552565,1552565,,C,T,ACA,ATA,Non-synonymous,Altering,SAR1461,SAR1461,penicillin-binding protein 2,1,0,0,C,SNP,0,C,1,C,1,1
P079,1557532,1557532,,T,C,GTA,GTG,Synonymous,Silent,SAR1465,SAR1465,putative asparaginyl-tRNA synthetase,0,0,1,B,SNP,0,T,1,T,1,1
P079,k31_var_171,1885301,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,G,1,1
P080,183626,183626,,G,T,GTG,TTG,Non-synonymous,Altering,SAR0165,SAR0165,capsular polysaccharide synthesis enzyme,1,0,0,C,SNP,0,G,1,G,1,1
P080,268390,268390,,T,C,TAC,TGC,Non-synonymous,Altering,SAR0227,SAR0227,putative acetyl-CoA transferase,0,0,1,B,SNP,0,T,1,T,1,1
P080,621528,621528,,G,A,GGA,GAA,Non-synonymous,Altering,SAR0567,SAR0567,bone sialoprotein-binding protein,1,0,0,C,SNP,0,G,1,G,1,1
P080,713319,713319,,C,A,CAA,AAA,Non-synonymous,Altering,SAR0666,SAR0666,hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P080,807328,807328,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P080,879525,879525,,G,A,CGC,CAC,Non-synonymous,Altering,SAR0833,SAR0833,putative membrane protein,1,0,0,C,SNP,0,G,1,G,1,1
P080,1472543,1472543,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,1,C,1,1
P080,1552547,1552547,,G,A,GGT,GAT,Non-synonymous,Altering,SAR1461,SAR1461,penicillin-binding protein 2,1,0,0,C,SNP,0,G,1,G,1,1
P080,1638569,1638569,,A,C,GGT,GGG,Synonymous,Silent,SAR1563,SAR1563,hypothetical protein,1,0,0,C,SNP,0,A,1,A,1,1
P080,1884219,1884219,,C,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,1,C,1,1
P080,2145345,2145345,,A,G,TTA,CTA,Synonymous,Silent,SAR2059,SAR2059,hypothetical phage protein,1,0,0,C,SNP,0,A,1,A,1,1
P080,2176815,2176815,,A,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P080,2266158,2266158,,A,T,ATA,AAA,Non-synonymous,Altering,SAR2198,SAR2198,putative ATP synthase protein I,1,0,0,C,SNP,0,A,1,A,1,1
P080,2330475,2330475,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P080,2385264,2385264,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,NA,NA,1
P080,2437328,2437328,,G,T,TCA,TAA,Nonsense,Truncating,SAR2367,SAR2367,putative inosine-uridine preferring nucleoside hydrolase,1,0,0,C,SNP,0,G,1,G,1,1
P080,2520404,2520404,,C,G,CGT,CCT,Non-synonymous,Altering,SAR2451,SAR2451,putative membrane protein,1,0,0,C,SNP,0,C,1,C,1,1
P080,2707509,2707509,,G,A,ACA,ATA,Non-synonymous,Altering,SAR2622,SAR2622,LysR family regulatory protein,1,0,0,C,SNP,0,G,1,G,1,1
P080,k31_var_24,1313476,,G,GG,GCT,GGC,"Frameshift, stop gained",Truncating,SAR1252,SAR1252,cell division protein FtsK,1,0,0,C,ShINDEL,1,NA,NA,GG,1,1
P080,k31_var_38,643644,,A,AA,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,AA,1,1
P080,k31_var_98,1053333,,C,CA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,C,1,1
P080,k61_var_32,1082309,,CTCTGTGTTGGGGCCCATCCTCAACTTGTACATTATTGTAAGCTGACTTTTCGTCAGCT,C,GAA,GAG,"Frameshift, stop gained",Truncating,SAR_RS05275,(no old locus tag),hypothetical protein,1,0,0,C,ShINDEL,58,NA,NA,CTCTGTGTTGGGGCCCATCCTCAACTTGTACATTATTGTAAGCTGACTTTTCGTCAGCT,1,1
P080,k61_var_34,618724,,AGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGATTCAGAAAGCGACTCAGACTCAGACAGCGACTCAGATTCAGACAGCGACTCAGACTCAGATAGTGATTCAGATTCAGACAGCGACTCAGATTCAGACAGCGACTCAGACTCAGAAAGCGACTCAGATTCAGACAGCGATTCAGAATCGGATAGC,A,GAC,GAC,"Non-synonymous, 70 codon deletion",Altering,SAR0566,SAR0566,serine-aspartate repeat-containing protein C,1,0,0,C,ShINDEL,210,NA,NA,AGACTCAGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGACAGCGACTCAGATTCAGAAAGCGACTCAGACTCAGACAGCGACTCAGATTCAGACAGCGACTCAGACTCAGATAGTGATTCAGATTCAGACAGCGACTCAGATTCAGACAGCGACTCAGACTCAGAAAGCGACTCAGATTCAGACAGCGATTCAGAATCGGATAGC,1,1
P080,k61_var_58,997641,,A,ATAATTTGCTTTGTAAATTAGACTGGAGATATATCTCCAGTC,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,41,NA,NA,A,1,1
P080,k61_var_59,2381869,,T,TTAATGTGCC,ATG,GGC,"Non-synonymous , 3 codon insertion",Altering,SAR2296,SAR2296,hypothetical protein,1,0,0,C,ShINDEL,9,NA,NA,ATAATTTGCTTTGTAAATTAGACTGGAGATATATCTCCAGTC,1,1
P080,k61_var_67,2693354,,C,CGAGGATTTAAACGCTATATTAGCGATATAC,AAT,GAG,"Non-synonymous, 10 codon insertion",Altering,SAR2609,SAR2609,N-acetyltransferase,0,0,1,B,ShINDEL,30,NA,NA,C,1,1
P081,2061235,2061235,,G,A,CTT,TTT,Non-synonymous,Altering,SAR1969,SAR1969,putative aminopeptidase,0,0,1,B,SNP,0,G,0,G,0,0
P081,2124798,2124798,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,0,G,0,0
P081,2618523,2618523,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,0,T,0,0
P081,k31_var_62,NA,"2585028(MSSA476, BX571857.1)",T,TT,GAT,AGA,"Frameshift, stop gained",Truncating,SAS2409,SAR2603,NAD(P)H-dependent oxidoreductase,0,0,1,B,ShINDEL,1,NA,NA,T,0,0
P082,582156,582156,,T,C,AAT,AAC,Synonymous,Silent,SAR0532,SAR0532,serine acetyltransferase,1,0,0,C,SNP,0,T,1,T,1,1
P082,891984,891984,,T,G,ATT,AGT,Non-synonymous,Altering,SAR0843,SAR0843,putative exported protein (pseudogene),1,0,0,C,SNP,0,T,1,T,1,1
P082,2237065,2237065,,G,A,GGC,GAC,Non-synonymous,Altering,SAR2166,SAR2166,sensor kinase protein,1,0,0,C,SNP,0,G,1,G,1,1
P083,k31_var_83,1193024,,T,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,A,1,1
P085,547528,547528,,T,A,GAT,GAA,Non-synonymous,Altering,SAR0509,SAR0509,putative RNA binding protein,1,0,0,C,SNP,0,T,1,T,1,1
P085,876645,876645,,C,T,ACA,ATA,Non-synonymous,Altering,SAR0831,SAR0831,"putative 2,3-bisphosphoglycerate-independent phosphoglycerate mutase",0,0,1,B,SNP,0,C,1,C,1,1
P085,1065046,1065046,,C,T,GTT,ATT,Non-synonymous,Altering,SAR1022,SAR1022,glutamyl endopeptidase precursor,1,0,0,C,SNP,0,C,1,C,1,1
P085,1532535,1532535,,T,C,ACG,GCG,Non-synonymous,Altering,SAR1447,SAR1447,very large surface anchored protein,1,0,0,C,SNP,0,T,1,T,1,1
P085,2562959,2562959,,T,C,GAA,GGA,Non-synonymous,Altering,SAR2489,SAR2489,nitrite reductase large subunit,1,0,0,C,SNP,0,T,1,T,1,1
P085,2567550,2567550,,T,A,AAT,ATT,Non-synonymous,Altering,SAR2493,SAR2493,putative nitrite transporter,1,0,0,C,SNP,0,T,1,NA,NA,1
P085,k31_var_63,1186250,,T,TT,ATT,AAT,"Frameshift, stop gained",Truncating,SAR1140,SAR1140,hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,T,1,1
P085,k31_var_67,468139,,GA,G,AAG,AGG,"Frameshift, stop gained",Truncating,SAR0438,SAR0438,ipoprotein,1,0,0,C,ShINDEL,1,NA,NA,G,1,1
P086,601224,601224,,G,T,GAT,TAT,Non-synonymous,Altering,SAR0552,SAR0552,translation elongation factor G,0,0,1,B,SNP,0,G,1,G,1,1
P086,630391,630391,,G,A,GGT,AGT,Non-synonymous,Altering,SAR0575,SAR0575,putative 6-phospho-3-hexuloisomerase,0,0,1,B,SNP,0,G,1,G,1,1
P086,1093280,1093280,,A,G,AAA,AAG,Synonymous,Silent,SAR1047,SAR1047,putative bifunctional purine biosynthesis protein [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase and IMP cyclohydrolase],1,0,0,C,SNP,0,A,1,A,1,1
P086,1264858,1264858,,C,T,GAC,GAT,Synonymous,Silent,SAR1213,SAR1213,signal recognition particle protein,0,0,1,B,SNP,0,C,1,C,1,1
P086,1480595,1480595,,C,A,GGA,GTA,Non-synonymous,Altering,SAR1423,SAR1423,hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P086,2074000,2074000,,C,T,GCG,GTG,Non-synonymous,Altering,SAR1985,SAR1985,DNA polymerase III subunit epsilon,0,0,1,B,SNP,0,C,1,C,1,1
P086,2183857,2183857,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,1,A,1,1
P086,2349379,2349379,,C,T,GCT,ACT,Non-synonymous,Altering,SAR2268,SAR2268,putative transport system binding lipoprotein,0,0,1,B,SNP,0,C,1,C,1,1
P086,2744703,2744703,,C,T,ATG,ATA,Non-synonymous,Altering,SAR2655,SAR2655,putative glyoxalase,1,0,0,C,SNP,0,C,1,C,1,1
P086,k31_var_23,995711,,T,C,TAT,CAT,Non-synonymous,Altering,SAR0952,SAR0952,putative oligopeptide transport ATP-binding protein,1,0,0,C,SNP,0,NA,NA,T,1,1
P086,k31_var_63,NA,"1251426(MSSA476, BX571857.1)",C,T,GAC,GAT,Synonymous,Silent,SAS1171,SAR1213,signal recognition particle protein,0,0,1,B,SNP,0,NA,NA,C,1,1
P088,853943,853943,,G,A,GAT,AAT,Non-synonymous,Altering,SAR0813,SAR0813,excinuclease ABC subunit A,0,0,1,B,SNP,0,G,1,G,1,1
P089,551617,551617,,G,A,GCA,ACA,Non-synonymous,Altering,SAR0512,SAR0512,putative cell division protein,1,0,0,C,SNP,0,G,1,G,1,1
P089,1577307,1577307,,C,G,GGT,GCT,Non-synonymous,Altering,SAR1484,SAR1484,putative GTPase,0,0,1,B,SNP,0,C,1,C,1,1
P089,1662585,1662585,,G,A,TCA,TTA,Non-synonymous,Altering,SAR1589,SAR1589,"6-phosphogluconate dehydrogenase, decarboxylating",1,0,0,C,SNP,0,G,1,G,1,1
P089,1893784,1893784,,C,T,GGA,GAA,Non-synonymous,Altering,SAR1814,SAR1814,catabolite control protein A,0,0,1,B,SNP,0,C,1,C,1,1
P089,2299777,2299777,,C,T,GAG,AAG,Non-synonymous,Altering,SAR2231,SAR2231,putative mannose-6-phosphate isomerase,1,0,0,C,SNP,0,C,1,C,1,1
P089,2415435,2415435,,T,C,ACA,ACG,Synonymous,Silent,SAR2342,SAR2342,putative membrane protein,1,0,0,C,SNP,0,T,1,T,1,1
P089,2834803,2834803,,C,T,TTG,TTA,Synonymous,Silent,SAR2730,SAR2730,conserved hypothetical protein,0,0,1,B,SNP,0,C,1,C,1,1
P089,k31_var_45,616242,,GA,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,AA,1,1
P090,14583,14583,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,0,G,0,0
P090,15394,15394,,A,G,ATG,GTG,Non-synonymous,Altering,SAR0010,SAR0010,putative membrane protein,0,0,1,B,SNP,0,A,0,A,0,0
P090,30432,30432,,C,T,AGC,AGT,Synonymous,Silent,SAR0022,SAR0022,metallo-beta-lactamase superfamily protein,0,1,0,D,SNP,0,C,1,C,1,1
P090,148224,148224,,A,G,TCA,TCG,Synonymous,Silent,SAR0134,SAR0134,polysaccharide biosynthesis protein,0,0,1,B,SNP,0,A,0,A,0,0
P090,150206,150206,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,0,A,0,0
P090,236344,236344,,C,A,GGA,GTA,Non-synonymous,Altering,SAR0203,SAR0203,putative phosphodiesterase,0,0,1,B,SNP,0,C,0,C,0,0
P090,273888,273888,,C,T,GTC,ATC,Non-synonymous,Altering,SAR0232,SAR0232,putative membrane protein,0,0,1,B,SNP,0,C,0,C,0,0
P090,307790,307790,,G,A,GTT,ATT,Non-synonymous,Altering,SAR0264,SAR0264,6-phospho-beta-glucosidase,0,0,1,B,SNP,0,G,1,G,1,1
P090,320656,320656,,T,C,GCA,GCG,Synonymous,Silent,SAR0276,SAR0276,putative membrane protein,0,1,0,D,SNP,0,T,1,T,1,1
P090,437500,437500,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,0,G,0,0
P090,450744,450744,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,0,C,0,0
P090,507130,507130,,C,G,AGC,AGG,Non-synonymous,Altering,SAR0474,SAR0474,putative glycosyl hydrolase,0,0,1,B,SNP,0,C,0,C,0,0
P090,600309,600309,,C,T,CAC,TAC,Non-synonymous,Altering,SAR0552,SAR0552,translation elongation factor G,0,0,1,B,SNP,0,C,1,C,1,1
P090,619474,619474,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,0,C,0,0
P090,635271,635271,,C,T,GCA,GTA,Non-synonymous,Altering,SAR0581,SAR0581,putative ketoacyl-CoA thiolase,0,0,1,B,SNP,0,C,0,C,0,0
P090,635520,635520,,G,A,GGG,GAG,Non-synonymous,Altering,SAR0581,SAR0581,putative ketoacyl-CoA thiolase,1,0,0,C,SNP,0,G,1,G,1,1
P090,672329,672329,,T,G,GTA,GGA,Non-synonymous,Altering,SAR0624,SAR0624,putative esterase,0,0,1,B,SNP,0,T,0,T,0,0
P090,795696,795696,,G,A,CCC,TCC,Non-synonymous,Altering,SAR0759,SAR0759,response regulator protein,0,1,0,D,SNP,0,G,1,G,1,1
P090,801240,801240,,C,T,GGC,GGT,Synonymous,Silent,SAR0767,SAR0767,para-aminobenzoate synthase component,1,0,0,C,SNP,0,C,1,C,1,1
P090,898888,898888,,G,A,TCC,TCT,Synonymous,Silent,SAR0852,SAR0852,putative membrane protein,0,0,1,B,SNP,0,G,0,G,0,0
P090,927166,927166,,T,C,ATT,GTT,Non-synonymous,Altering,SAR0889,SAR0889,conserved hypothetical protein,0,0,1,B,SNP,0,T,0,T,0,0
P090,954168,954168,,C,T,GCA,GTA,Non-synonymous,Altering,SAR0919,SAR0919,ornithine aminotransferase,0,1,0,D,SNP,0,C,1,C,1,1
P090,994709,994709,,C,T,ACA,ATA,Non-synonymous,Altering,SAR0951,SAR0951,putative oligopeptide transport ATP-binding protein,0,0,1,B,SNP,0,C,0,C,0,0
P090,995029,995029,,G,A,AAG,AAA,Synonymous,Silent,SAR0952,SAR0952,putative oligopeptide transport ATP-binding protein,0,0,1,B,SNP,0,G,1,G,1,1
P090,1038649,1038649,,G,A,GGA,AGA,Non-synonymous,Altering,SAR0992,SAR0992,putative protease,0,0,1,B,SNP,0,G,0,G,0,0
P090,1083334,1083334,,T,C,GTA,GTG,Synonymous,Silent,SAR1037,SAR1037,FolD bifunctional protein [includes: methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase],0,0,1,B,SNP,0,T,1,T,1,1
P090,1191573,1191573,,T,G,TTA,GTA,Non-synonymous,Altering,SAR1146,SAR1146,putative membrane protein,0,0,1,B,SNP,0,T,0,T,0,0
P090,1199665,1199665,,T,C,TTT,TCT,Non-synonymous,Altering,SAR1157,SAR1157,penicillin-binding protein 1,0,1,0,D,SNP,0,T,1,T,1,1
P090,1238711,1238711,,C,T,GCA,GTA,Non-synonymous,Altering,SAR1189,SAR1189,putative lipoprotein,0,1,0,D,SNP,0,C,1,C,1,1
P090,1244288,1244288,,C,T,GCA,GTA,Non-synonymous,Altering,SAR1195,SAR1195,putative protein phosphatase,0,1,0,D,SNP,0,C,1,C,1,1
P090,1252225,1252225,,T,A,TCA,ACA,Non-synonymous,Altering,SAR1203,SAR1203,ATP-dependent DNA helicase,0,0,1,B,SNP,0,T,0,T,0,0
P090,1326245,1326245,,G,A,GGT,AGT,Non-synonymous,Altering,SAR1264,SAR1264,conserved hypothetical protein,0,1,0,D,SNP,0,G,1,G,1,1
P090,1344956,1344956,,C,T,GAC,GAT,Synonymous,Silent,SAR1279,SAR1279,conserved hypothetical protein,0,0,1,B,SNP,0,C,0,C,0,0
P090,1365487,1365487,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,0,A,0,0
P090,1445782,1445782,,A,G,GCA,GCG,Synonymous,Silent,SAR1387,SAR1387,factor essential for expression of methicillin resistance,0,0,1,B,SNP,0,A,0,A,0,0
P090,1484153,1484153,,G,T,CCG,ACG,Non-synonymous,Altering,SAR1425,SAR1425,2-oxoglutarate dehydrogenase E1 component,0,0,1,B,SNP,0,G,1,G,1,1
P090,1657397,1657397,,C,G,ATG,ATC,Non-synonymous,Altering,SAR1585,SAR1585,maltose operon transcriptional repressor,0,0,1,B,SNP,0,C,0,C,0,0
P090,1726369,1726369,,T,C,CAT,CGT,Non-synonymous,Altering,SAR1658,SAR1658,GrpE protein (Hsp-70 cofactor),0,0,1,B,SNP,0,T,0,T,0,0
P090,1740985,1740985,,A,G,CAT,CAC,Synonymous,Silent,SAR1675,SAR1675,conserved hypothetical protein,0,0,1,B,SNP,0,A,0,A,0,0
P090,1765892,1765892,,G,A,GCA,GTA,Non-synonymous,Altering,SAR1702,SAR1702,putative cysteine desulfurase,1,0,0,C,SNP,0,G,1,G,1,1
P090,1818055,1818055,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,C,1,C,1,1
P090,1870849,1870849,,T,C,ATT,ACT,Non-synonymous,Altering,SAR1796,SAR1796,conserved hypothetical protein,0,0,1,B,SNP,0,T,0,T,0,0
P090,1880249,1880249,,T,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,T,1,1
P090,1888687,1888687,,G,A,TTC,TTT,Synonymous,Silent,SAR1810,SAR1810,formate--tetrahydrofolate,0,0,1,B,SNP,0,G,0,G,0,0
P090,1924963,1924963,,G,A,GAC,GAT,Synonymous,Silent,SAR1841,SAR1841,putative surface anchored protein,0,0,1,B,SNP,0,G,0,G,0,0
P090,2041593,2041593,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,0,A,0,0
P090,2104515,2104515,,C,T,ACA,ATA,Non-synonymous,Altering,SAR2011,SAR2011,isochorismatase family protein,0,1,0,D,SNP,0,C,1,C,1,1
P090,2143254,2143254,,C,T,GAT,AAT,Non-synonymous,Altering,SAR2053,SAR2053,hypothetical phage protein,0,0,1,B,SNP,0,C,0,C,0,0
P090,2186667,2186667,,A,T,TTA,TTT,Non-synonymous,Altering,SAR2126,SAR2126,autoinducer sensor protein response regulator protein,0,1,0,D,SNP,0,A,1,A,1,1
P090,2255380,2255380,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,0,C,0,0
P090,2264243,2264243,,T,G,AAA,ACA,Non-synonymous,Altering,SAR2194,SAR2194,putative ATP synthase delta chain,0,1,0,D,SNP,0,T,1,T,1,1
P090,2267993,2267993,,A,C,GTT,GGT,Non-synonymous,Altering,SAR2200,SAR2200,uracil phosphoribosyltransferase,0,0,1,B,SNP,0,A,0,A,0,0
P090,2311264,2311264,,A,G,GAT,GAC,Synonymous,Silent,SAR2242,SAR2242,glucosamine--fructose-6-phosphate aminotransferase [isomerizing],0,1,0,D,SNP,0,A,1,A,1,1
P090,2407853,2407853,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,0,T,0,0
P090,2421844,2421844,,T,A,CAA,CAT,Non-synonymous,Altering,SAR2348,SAR2348,hypothetical protein,0,0,1,B,SNP,0,T,0,T,0,0
P090,2436154,2436154,,A,T,CGT,CGA,Synonymous,Silent,SAR2366,SAR2366,BioY family protein,0,1,0,D,SNP,0,T,1,NA,NA,1
P090,2484278,2484278,,A,G,GTA,GCA,Non-synonymous,Altering,SAR2416,SAR2416,putative imidazolonepropionase,0,0,1,B,SNP,0,G,0,G,0,0
P090,2515408,2515408,,C,T,GAA,AAA,Non-synonymous,Altering,SAR2446,SAR2446,putative permease protein,0,1,0,D,SNP,0,C,1,C,1,1
P090,2550620,2550620,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,T,1,1
P090,2575506,2575506,,C,T,CCG,CCA,Synonymous,Silent,SAR2503,SAR2503,transport system membrane protein,0,0,1,B,SNP,0,C,0,C,0,0
P090,2614943,2614943,,G,A,TCG,TTG,Non-synonymous,Altering,SAR2535,SAR2535,putative glycine betaine/carnitine/choline transport system permease protein,0,0,1,B,SNP,0,G,0,G,0,0
P090,2692096,2692096,,C,T,GGG,GGA,Synonymous,Silent,SAR2607,SAR2607,putative haloacid dehalogenase-like hydrolase,0,0,1,B,SNP,0,C,0,C,0,0
P090,2731712,2731712,,C,T,GAT,AAT,Non-synonymous,Altering,SAR2642,SAR2642,squalene synthase,0,0,1,B,SNP,0,C,0,C,0,0
P090,2804734,2804734,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,0,T,0,0
P090,2818817,2818817,,C,T,TCG,TTG,Non-synonymous,Altering,SAR2720,SAR2720,"putative PTS transport system, IIABC component",0,0,1,B,SNP,0,C,0,C,0,0
P090,2839585,2839585,,A,G,TCC,CCC,Non-synonymous,Altering,SAR2734,SAR2734,serine-rich adhesin for platelets,0,0,1,B,SNP,0,A,1,A,1,1
P090,2842797,2842797,,G,A,ACA,ATA,Non-synonymous,Altering,SAR2734,SAR2734,serine-rich adhesin for platelets,0,1,0,D,SNP,0,G,1,G,1,1
P090,2866535,2866535,,T,C,GAA,GGA,Non-synonymous,Altering,SAR2763,SAR2763,putative lipoprotein,0,0,1,B,SNP,0,T,1,T,1,1
P090,2869941,2869941,,C,A,GAT,TAT,Non-synonymous,Altering,SAR2766,SAR2766,ABC transporter ATP-binding protein,1,0,0,C,SNP,0,C,1,C,1,1
P090,2895983,2895983,,C,T,TTG,TTA,Synonymous,Silent,SAR2793,SAR2793,putative membrane protein,0,1,0,D,SNP,0,C,1,C,1,1
P090,1042859(self),NA,"843388(MSSA476, BX571857.1)",T,A,AGT,AGA,Non-synonymous,Altering,SAS0752,SAR0842,clumping factor A,0,0,1,B,SNP,0,NA,NA,T,0,0
P090,1059578(self),907478,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,C,0,0
P090,2039519(self),NA,unknown,T,C,AGG,GGG,Non-synonymous,Altering,"(RAST, CDS NA)",(no ortholog),serine protease,1,0,0,C,SNP,0,NA,NA,T,1,1
P090,2237554(self),NA,"2088428(MSSA476, BX571857.1)",G,C,GAT,CAT,Non-synonymous,Altering,SAS1943,SAR2125,accessory gene regulator protein C,0,0,1,B,SNP,0,NA,NA,G,0,0
P090,2440168(self),NA,unknown,C,T,ATG,ATA,Non-synonymous,Altering,"(RAST, CDS NA)",(no ortholog),ClpB protein,0,0,1,B,SNP,0,NA,NA,T,0,0
P090,2442485(self),NA,unknown,C,A,GGT,TGT,Non-synonymous,Altering,"(RAST, CDS NA)",(no ortholog),putative helicase,0,0,1,B,SNP,0,NA,NA,C,1,1
P090,2712435(self),NA,"2548253(MSSA476, BX571857.1)",G,A,CCA,TCA,Non-synonymous,Altering,SAS2382,(no ortholog),MFS transporter,1,0,0,C,SNP,0,NA,NA,G,1,1
P090,486293(self),NA,"270010(MSSA476, BX571857.1)",G,T,GAT,TAT,Non-synonymous,Altering,SAS0229,SAR0248,hypothetical protein,0,0,1,B,SNP,0,NA,NA,G,0,0
P090,493764(self),NA,"278079(MSSA476, BX571857.1)",A,G,CCA,CCG,Synonymous,Silent,SAS0234,SAR0254,hypothetical protein,0,0,1,B,SNP,0,NA,NA,A,1,1
P090,k31_var_101,NA,"1821376(MSSA476, BX571857.1)",G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,G,0,0
P090,k31_var_114,1540768,,CATTA,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,4,NA,NA,C,0,0
P090,k31_var_117,165787,,G,GA,GGG,GGA,"Frameshift, stop gained",Truncating,SAR_RS00735,SAR0150,putative aldehyde-alcohol dehydrogenase,0,1,0,D,ShINDEL,1,NA,NA,G,1,1
P090,k31_var_121,665834,,A,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,T,1,1
P090,k31_var_125,NA,"1901774(MSSA476, BX571857.1)",T,TTATTTT,TTA,TTT,"Non-synonymous, 2 codon insertion",Altering,SAS1751,SAR1914,hypothetical protein,0,0,1,B,ShINDEL,6,NA,NA,T,1,1
P090,k31_var_134,783550,,T,TAGAGCAAAATTGAA,CAT,CAT,"Frameshift, stop gained",Truncating,SAR0748,SAR0748,MFS transporter,0,0,1,B,ShINDEL,14,NA,NA,TAGAGCAAAATTGAA,0,0
P090,k31_var_145,2437821,,A,AA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,AA,0,0
P090,k31_var_154,1308106,,T,TA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,TA,0,0
P090,k31_var_167,2126257,,AA,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,A,0,0
P090,k31_var_1888,1719710,,A,AA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,ShINDEL,1,NA,NA,A,1,1
P090,k31_var_60,2902235,,A,AC,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,AC,1,1
P090,k31_var_8953,2737442,,C,CA,TTG,TTT,"Frameshift, stop gained",Truncating,SAR2649,SAR2649,O-acetyltransferase OatA,0,1,0,D,ShINDEL,1,NA,NA,C,1,1
P090,k31_var_8954,1814091,,T,TATTAGTATAATGTGTC,AAG,AGG,"Frameshift, stop gained",Truncating,SAR1751,SAR1751,cytochrome C assembly protein,0,1,0,D,ShINDEL,16,NA,NA,TATTAGTATAATGTGTC,0,1
P090,k61_var_185,2002334,,G,A,GCA,GAA,Non-synonymous,Altering,SAR1922,SAR1922,alpha/beta hydrolase,0,1,0,D,SNP,0,NA,NA,G,1,1
P090,k61_var_197,NA,"1901938(H-EMRSA-15, NZ_CP007659.1)",GCTTTGC,GTTTTGA,CGC,CGT,Non-synonymous,Altering,ER16_RS09315,(no ortholog),calcium-binding protein,0,1,0,D,SNP,0,NA,NA,GCTTTGC,1,1
P090,k61_var_79,2802397,,ATCTGAGTCTGAATCGCTG,A,GAC,GAA,"Non-synonymous, 6 codon deletion",Altering,SAR2709,SAR2709,clumping factor B,0,0,1,B,ShINDEL,18,NA,NA,A,0,0
P090,k61_var_96,NA,"2700455(MSSA476, BX571857.1)",G,T,CAG,CAT,Non-synonymous,Altering,SAS2516,SAR2709,clumping factor B,0,0,1,B,SNP,0,NA,NA,G,1,1
P091,950751,950751,,C,T,CAC,TAC,Non-synonymous,Altering,SAR0916,SAR0916,putative cyclophilin type peptidyl-prolyl cis-trans isomerase,0,1,0,D,SNP,0,C,1,C,1,1
P091,k31_var_124,2183350,,C,T,NA,NA,Intergenic,Intergenic,NA,NA, last base in RNAIII regulatory transcript,0,1,0,D,SNP,0,NA,NA,C,1,1
P092,1690604,1690604,,G,A,TCT,TTT,Non-synonymous,Altering,SAR1620,SAR1620,putative membrane protein,0,1,0,D,SNP,0,G,1,G,1,1
P092,2857472,2857472,,G,A,GCG,GTG,Non-synonymous,Altering,SAR2753,SAR2753,lipase precursor,1,0,0,C,SNP,0,G,1,G,1,1
P092,k31_var_13223,585408,,GA,G,ATA,TAC,Frameshift with readthrough,Altering,SAR0536,SAR0536,hypothetical protein,0,1,0,D,ShINDEL,1,NA,NA,GA,1,1
P093,353493,353493,,C,T,ACA,ATA,Non-synonymous,Altering,SAR0310,SAR0310,putative nucleoside permease,0,1,0,D,SNP,0,C,1,C,1,1
P093,446847,446847,,G,A,CAC,CAT,Synonymous,Silent,SAR0411,SAR0411,hypothetical protein,0,1,0,D,SNP,0,G,1,G,1,1
P093,1145103,1145103,,G,A,ACA,ATA,Non-synonymous,Altering,SAR1099,SAR1099,conserved hypothetical protein,0,1,0,D,SNP,0,G,1,G,1,1
P093,1694584,1694584,,G,A,ACT,ATT,Non-synonymous,Altering,SAR1626,SAR1626,putative membrane protein,0,1,0,D,SNP,0,G,1,G,1,1
P093,2005403,2005403,,G,A,ACG,ATG,Non-synonymous,Altering,SAR1925,SAR1925,uroporphyrinogen decarboxylase,1,0,0,C,SNP,0,G,1,G,1,1
P093,2737039,2737039,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P093,374650(self),455731,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,A,1,1
P093,k31_var_69,NA,"34014(6850, NC_022222.1)",A,AA,AAT,AAA,"Frameshift, stop gained",Truncating,RSAU_RS00135,(no ortholog),hypothetical protein,1,0,0,C,ShINDEL,1,NA,NA,AA,1,1
P093,k31_var_85,448293,,CT,C,AGA,GAT,"Frameshift, stop gained",Truncating,SAR_RS02075,(no ortholog),mRNA interferase PemK,1,0,0,C,ShINDEL,1,NA,NA,CT,1,1
P093,k61_var_163,NA,"41595(USA300_2014.C02 plasmid, NZ_CP012121.1)",CGTCCAGAAGTTCGAAAATCGAAC,C,ACG,ACG,"Frameshift, stop gained",Truncating,ACO02_2826,(no ortholog),hypothetical protein,0,1,0,D,ShINDEL,23,NA,NA,C,0,0
P093,k61_var_51,890355,,A,ATAGCGATTCAGACTCAGA,GAA,GAC,"Non-synonymous, 6 codon insertion",Altering,SAR0842,SAR0842,clumping factor A,0,0,1,B,ShINDEL,18,NA,NA,ATAGCGATTCAGACTCAGA,0,0
P094,770908,770908,,T,C,TTT,CTT,Non-synonymous,Altering,SAR0737,SAR0737,ABC transporter ATP-binding protein,1,0,0,C,SNP,0,T,1,T,1,1
P094,868304,868304,,C,T,GCG,GTG,Non-synonymous,Altering,SAR0824,SAR0824,putative malolactic enzyme,1,0,0,C,SNP,0,C,1,C,1,1
P094,1179759,1179759,,T,C,AAT,AGT,Non-synonymous,Altering,SAR1134,SAR1134,hypothetical protein,1,0,0,C,SNP,0,T,1,T,1,1
P094,1888196,1888196,,T,C,GAT,GGT,Non-synonymous,Altering,SAR1810,SAR1810,formate--tetrahydrofolate ligase,1,0,0,C,SNP,0,T,1,T,1,1
P094,2193459,2193459,,C,T,GGT,GAT,Non-synonymous,Altering,SAR2132,SAR2132,putative membrane protein,1,0,0,C,SNP,0,C,1,C,1,1
P095,242689,242689,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P095,366017,366017,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P095,770277,770277,,G,T,CCA,CAA,Non-synonymous,Altering,SAR0736,SAR0736,putative undecaprenol kinase,1,0,0,C,SNP,0,G,1,G,1,1
P095,1036016,1036016,,A,G,CAC,CGC,Non-synonymous,Altering,SAR0990,SAR0990,peptide chain release factor 3,1,0,0,C,SNP,0,A,1,A,1,1
P095,1046363,1046363,,C,T,TCA,TTA,Non-synonymous,Altering,SAR0999,SAR0999,putative membrane protein,1,0,0,C,SNP,0,C,1,C,1,1
P095,1141876,1141876,,A,G,ATG,ACG,Non-synonymous,Altering,SAR1094,SAR1094,putative exported protein,1,0,0,C,SNP,0,A,1,A,1,1
P095,1308194,1308194,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P095,1809191,1809191,,T,C,ATA,ATG,Non-synonymous,Altering,SAR1745,SAR1745,putative membrane protein,0,0,1,B,SNP,0,T,1,T,1,1
P095,1934629,1934629,,G,A,ACA,ATA,Non-synonymous,Altering,SAR1844,SAR1844,putative membrane protein,1,0,0,C,SNP,0,G,1,G,1,1
P095,1991565,1991565,,G,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P095,2193756,2193756,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P095,2270030,2270030,,T,C,AGT,GGT,Non-synonymous,Altering,SAR2202,SAR2202,conserved hypothetical protein,1,0,0,C,SNP,0,T,1,T,1,1
P095,2276831,2276831,,T,C,TAT,TGT,Non-synonymous,Altering,SAR2210,SAR2210,aldehyde dehydrogenase family protein,1,0,0,C,SNP,0,T,1,T,1,1
P095,2285738,2285738,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,T,1,1
P095,2347144,2347144,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P095,2354660,2354660,,T,C,CTA,CTG,Synonymous,Silent,SAR2271,SAR2271,putative membrane protein,1,0,0,C,SNP,0,T,1,T,1,1
P095,2528676,2528676,,C,T,GGT,AGT,Non-synonymous,Altering,SAR2457,SAR2457,putative lipoprotein,1,0,0,C,SNP,0,C,1,C,1,1
P095,2535304,2535304,,T,C,TAT,CAT,Non-synonymous,Altering,SAR2464,SAR2464,TetR family regulatory protein,1,0,0,C,SNP,0,T,1,T,1,1
P095,2563388,2563388,,T,C,GAA,GGA,Non-synonymous,Altering,SAR2489,SAR2489,nitrite reductase large subunit,1,0,0,C,SNP,0,T,1,T,1,1
P095,k31_var_140,2105875,,TT,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,T,1,1
P095,k31_var_237,794110,,AA,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,ShINDEL,1,NA,NA,AA,1,1
P095,k31_var_54,NA,"838095(MSSA476, BX571857.1)",AT,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,AT,1,1
P096,126181,126181,,C,T,AGT,AAT,Non-synonymous,Altering,SAR0115,SAR0115,putative regulatory protein,0,0,1,B,SNP,0,C,1,C,1,1
P096,237411,237411,,A,G,TTA,TTG,Synonymous,Silent,SAR0204,SAR0204,putative peptidase,0,0,1,B,SNP,0,A,0,A,0,0
P096,389344,389344,,A,G,TTT,TTC,Synonymous,Silent,SAR0343,SAR0343,putative Sec-independent protein translocase protein,0,0,1,B,SNP,0,G,0,G,0,0
P096,513933,513933,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P096,706487,706487,,T,C,GTG,GCG,Non-synonymous,Altering,SAR0659,SAR0659,ferrichrome transport permease,0,0,1,B,SNP,0,T,1,T,1,1
P096,793012,793012,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,0,G,0,0
P096,864192,864192,,C,T,ACG,ATG,Non-synonymous,Altering,SAR0821,SAR0821,conserved hypothetical protein,0,0,1,B,SNP,0,C,1,C,1,1
P096,879571,879571,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,G,1,G,1,1
P096,1128763,1128763,,C,T,GCT,GTT,Non-synonymous,Altering,SAR1083,SAR1083,BipA family GTPase,0,0,1,B,SNP,0,C,0,C,0,0
P096,1278115,1278115,,G,A,GTG,ATG,Non-synonymous,Altering,SAR1225,SAR1225,SMF family protein,0,0,1,B,SNP,0,G,1,G,1,1
P096,1321496,1321496,,C,A,CCA,CAA,Non-synonymous,Altering,SAR1260,SAR1260,conserved hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P096,1333221,1333221,,G,C,GTA,CTA,Non-synonymous,Altering,SAR1271,SAR1271,DNA mismatch repair protein MutS,0,1,0,D,SNP,0,G,1,G,1,1
P096,1474881,1474881,,C,T,GCT,GTT,Non-synonymous,Altering,SAR1418,SAR1418,conserved hypothetical protein,0,0,1,B,SNP,0,C,0,C,0,0
P096,2017624,2017624,,G,C,CCA,CGA,Non-synonymous,Altering,SAR1935,SAR1935,putative DNA repair exonuclease,0,0,1,B,SNP,0,G,1,G,1,1
P096,2071950,2071950,,T,C,AGA,AGG,Synonymous,Silent,SAR1983,SAR1983,Mur ligase family protein,1,0,0,C,SNP,0,T,1,T,1,1
P096,2212974,2212974,,T,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,T,1,1
P096,2239043,2239043,,G,T,CGC,AGC,Non-synonymous,Altering,SAR2168,SAR2168,putative helicase,0,1,0,D,SNP,0,G,1,G,1,1
P096,2314520,2314520,,T,A,CTT,CAT,Non-synonymous,Altering,SAR2245,SAR2245,putative transcriptional antiterminator,0,0,1,B,SNP,0,T,1,T,1,1
P096,2327726,2327726,,C,T,GTA,ATA,Non-synonymous,Altering,SAR2252,SAR2252,putative phosphoglucosamine mutase,0,0,1,B,SNP,0,C,0,C,0,0
P096,2416284,2416284,,C,T,CTC,CTT,Synonymous,Silent,SAR2344,SAR2344,putative membrane protein,0,0,1,B,SNP,0,C,0,C,0,0
P096,2636379,2636379,,A,G,AGT,AGC,Synonymous,Silent,SAR2554,SAR2554,oligopeptide transporter putative substrate binding domain,0,0,1,B,SNP,0,A,0,A,0,0
P096,2743413,2743413,,G,A,GAG,AAG,Non-synonymous,Altering,SAR2653,SAR2653,hypothetical protein,0,1,0,D,SNP,0,G,1,G,1,1
P096,2754023,2754023,,A,G,TCA,CCA,Non-synonymous,Altering,SAR2667,SAR2667,hypothetical protein,0,0,1,B,SNP,0,A,0,A,0,0
P096,2792763,2792763,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,C,0,C,0,0
P096,2698597(self),9687,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,T,1,T,1,1
P096,2779(self),NA,"82056(MSSA476, BX571857.1)",A,C,GCA,GAA,Non-synonymous,Altering,SAS0073,SAR0106,putative lipoprotein,1,0,0,C,SNP,0,NA,NA,A,1,1
P096,2783(self),NA,"82059(MSSA476, BX571857.1))",G,A,AAA,AAG,Synonymous,Silent,SAS0073,SAR0106,putative lipoprotein,0,0,1,B,SNP,0,NA,NA,NA,NA,NA
P096,3582(self),110834,,G,A,ATA,ATG,Non-synonymous,Altering,SAS0074,SAR0106,putative lipoprotein,0,0,1,B,SNP,0,NA,NA,NA,NA,NA
P096,k31_var_135,1751472,,C,CT,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,CT,0,0
P096,k31_var_151,2475841,,A,AGT,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,2,NA,NA,AGT,0,0
P096,k31_var_153,2350423,,C,CTA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,2,NA,NA,C,1,1
P096,k31_var_63,NA,"1251426(MSSA476, BX571857.1)",AA,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,AA,1,1
P097,2591962,2591962,,A,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P097,k31_var_48,1377933,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,C,1,1
P098,490161,490161,,C,T,CTC,TTC,Non-synonymous,Altering,SAR0461,SAR0461,ABC transporter ATP-binding protein,0,0,1,B,SNP,0,C,1,C,1,1
P098,539745,539745,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,T,1,T,1,1
P098,791018,791018,,T,C,TTG,TCG,Non-synonymous,Altering,SAR0755,SAR0755,putative membrane protein,0,0,1,B,SNP,0,T,1,T,1,1
P098,1691305,1691305,,C,T,GTT,ATT,Non-synonymous,Altering,SAR1621,SAR1621,hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P098,1829977,1829977,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,A,1,A,1,1
P098,2373038,2373038,,C,A,TGC,TTC,Non-synonymous,Altering,SAR2289,SAR2289,hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P098,2591971,2591971,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,1,0,D,SNP,0,C,1,C,1,1
P098,k31_var_73,1926933,,G,GT,CAA,CAA,"Frameshift, stop gained",Truncating,sasC,SAR1841,putative surface anchored protein,0,0,1,B,ShINDEL,1,NA,NA,GT,0,0
P099,267633,267633,,A,G,TGT,TGC,Synonymous,Silent,SAR0227,SAR0227,putative acetyl-CoA transferase,0,1,0,D,SNP,0,A,1,A,1,1
P099,525704,525704,,G,A,CGC,CAC,Non-synonymous,Altering,SAR0487,SAR0487,conserved hypothetical protein,0,0,1,B,SNP,0,G,0,G,0,0
P099,1210113,1210113,,G,A,GCG,GCA,Synonymous,Silent,SAR1164,SAR1164,conserved hypothetical protein,0,1,0,D,SNP,0,G,1,G,1,1
P099,1482919,1482919,,G,A,CTT,TTT,Non-synonymous,Altering,SAR1424,SAR1424,dihydrolipoamide succinyltransferase E2 component of 2-oxoglutarate dehydrogenase complex,0,0,1,B,SNP,0,G,0,G,0,0
P099,2062360,2062360,,G,T,GGG,GTG,Non-synonymous,Altering,SAR1971,SAR1971,low molecular weight phosphotyrosine protein phosphatase,1,0,0,C,SNP,0,G,1,G,1,1
P099,2820832,2820832,,C,A,GTT,TTT,Non-synonymous,Altering,SAR2722,SAR2722,putative membrane protein,0,1,0,D,SNP,0,C,1,C,1,1
P100,908951,908951,,C,A,CAA,AAA,Non-synonymous,Altering,SAR0870,SAR0870,ABC transporter ATP-binding protein,1,0,0,C,SNP,0,C,1,C,1,1
P100,1899670,1899670,,T,C,GGA,GGG,Synonymous,Silent,SAR1818,SAR1818,UDP-N-acetylmuramate--alanine ligase,1,0,0,C,SNP,0,T,1,T,1,1
P101,143935,143935,,T,C,ATT,ATC,Synonymous,Silent,SAR0130,SAR0130,NAD dependent epimerase/dehydratase family protein,1,0,0,C,SNP,0,T,1,T,1,1
P101,167357,167357,,C,T,CTT,TTT,Non-synonymous,Altering,SAR0150,SAR0150,putative aldehyde-alcohol dehydrogenase,0,1,0,D,SNP,0,C,1,C,1,1
P101,250097,250097,,G,T,CGC,CGA,Synonymous,Silent,SAR0215,SAR0215,putative sensor kinase protein,1,0,0,C,SNP,0,G,1,G,1,1
P101,281038,281038,,A,C,GAT,GCT,Non-synonymous,Altering,SAR0238,SAR0238,putative PTS multi-domain regulator (pseudogene),1,0,0,C,SNP,0,C,1,C,1,1
P101,327101,327101,,G,T,AAG,AAT,Non-synonymous,Altering,SAR0280,SAR0280,putative membrane protein,1,0,0,C,SNP,0,G,1,G,1,1
P101,357466,357466,,G,T,AAG,AAT,Non-synonymous,Altering,SAR0313,SAR0313,putative ROK family protein,1,0,0,C,SNP,0,G,1,G,1,1
P101,375651,375651,,G,T,GGC,GGA,Synonymous,Silent,SAR0329,SAR0329,putative PTS multidomain regulator,1,0,0,C,SNP,0,G,1,G,1,1
P101,389451,389451,,G,T,CAA,AAA,Non-synonymous,Altering,SAR0343,SAR0343,putative Sec-independent protein translocase protein,1,0,0,C,SNP,0,G,1,G,1,1
P101,434925,434925,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P101,441591,441591,,T,A,CTG,CAG,Non-synonymous,Altering,SAR0406,SAR0406,putative xanthine phosphoribosyltransferase,1,0,0,C,SNP,0,T,1,T,1,1
P101,810199,810199,,T,C,GAT,GAC,Synonymous,Silent,SAR0774,SAR0774,putative ATP-dependent DNA helicase,1,0,0,C,SNP,0,C,1,C,1,1
P101,836265,836265,,C,A,GAT,TAT,Non-synonymous,Altering,SAR0798,SAR0798,putative membrane protein,1,0,0,C,SNP,0,C,1,C,1,1
P101,852740,852740,,G,A,GGC,GAC,Non-synonymous,Altering,SAR0812,SAR0812,excinuclease ABC subunit B,1,0,0,C,SNP,0,G,1,G,1,1
P101,901138,901138,,G,T,AGC,AGA,Non-synonymous,Altering,SAR0857,SAR0857,putative LysE type translocator protein,0,1,0,D,SNP,0,G,1,G,1,1
P101,931221,931221,,G,T,GAT,TAT,Non-synonymous,Altering,SAR0894,SAR0894,D-alanine-D-alanyl carrier protein ligase,1,0,0,C,SNP,0,G,1,G,1,1
P101,955617,955617,,G,A,CGC,CAC,Non-synonymous,Altering,SAR0920,SAR0920,putative NAD-specific glutamate dehydrogenase,1,0,0,C,SNP,0,G,1,G,1,1
P101,1003277,1003277,,G,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,G,1,G,1,1
P101,1036643,1036643,,C,A,CTT,ATT,Non-synonymous,Altering,SAR0991,SAR0991,putative membrane protein,1,0,0,C,SNP,0,C,1,C,1,1
P101,1134121,1134121,,A,G,AAA,GAA,Non-synonymous,Altering,SAR1088,SAR1088,putative pyruvate carboxylase,1,0,0,C,SNP,0,A,1,A,1,1
P101,1137970,1137970,,C,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P101,1152315,1152315,,C,A,GCT,GAT,Non-synonymous,Altering,SAR1106,SAR1106,putative transport system extracellular binding lipoprotein,1,0,0,C,SNP,0,C,1,C,1,1
P101,1300324,1300324,,C,T,ACA,ATA,Non-synonymous,Altering,SAR1241,SAR1241,conserved hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P101,1302730,1302730,,G,T,GCA,TCA,Non-synonymous,Altering,SAR1245,SAR1245,translation initiation factor IF-2,1,0,0,C,SNP,0,G,1,G,1,1
P101,1309079,1309079,,G,T,GAT,TAT,Non-synonymous,Altering,SAR1250,SAR1250,polyribonucleotide nucleotidyltransferase,1,0,0,C,SNP,0,G,1,G,1,1
P101,1311678,1311678,,C,G,CAT,GAT,Non-synonymous,Altering,SAR1251,SAR1251,conserved hypothetical protein,1,0,0,C,SNP,0,C,1,C,1,1
P101,1337892,1337892,,T,C,GTT,GCT,Non-synonymous,Altering,SAR1273,SAR1273,putative glycerol uptake operon antiterminator regulatory protein,1,0,0,C,SNP,0,T,1,T,1,1
P101,1416934,1416934,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P101,1468182,1468182,,G,T,GAG,GAT,Non-synonymous,Altering,SAR1409,SAR1409,"putative tetrahydrodipiCOL, NC_002951.2inate acetyltransferase",1,0,0,C,SNP,0,G,1,G,1,1
P101,1485713,1485713,,C,T,GTC,ATC,Non-synonymous,Altering,SAR1425,SAR1425,2-oxoglutarate dehydrogenase E1 component,0,1,0,D,SNP,0,C,1,C,1,1
P101,1486881,1486881,,C,A,GGA,GTA,Non-synonymous,Altering,SAR1426,SAR1426,sensor kinase protein,1,0,0,C,SNP,0,C,1,C,1,1
P101,1561574,1561574,,C,A,GTG,TTG,Non-synonymous,Altering,SAR1467,SAR1467,BirA bifunctional protein [includes: biotin operon repressor; biotin--[acetyl-CoA-carboxylase] synthetase,1,0,0,C,SNP,0,C,1,C,1,1
P101,1572709,1572709,,T,C,GAT,GGT,Non-synonymous,Altering,SAR1478,SAR1478,putative nucleoside diphosphate kinase,1,0,0,C,SNP,0,T,1,T,1,1
P101,1650361,1650361,,G,T,GCA,TCA,Non-synonymous,Altering,SAR1579,SAR1579,putative pyrroline-5-carboxylate reductase,1,0,0,C,SNP,0,G,1,G,1,1
P101,1651665,1651665,,A,G,GGT,GGC,Synonymous,Silent,SAR1581,SAR1581,conserved hypothetical protein,1,0,0,C,SNP,0,A,1,A,1,1
P101,1669106,1669106,,C,A,AAG,AAT,Non-synonymous,Altering,SAR1595,SAR1595,2-oxoisovalerate dehydrogenase alpha subunit,1,0,0,C,SNP,0,C,1,C,1,1
P101,1718925,1718925,,C,A,GGC,GTC,Non-synonymous,Altering,SAR1651,SAR1651,putative membrane protein,1,0,0,C,SNP,0,C,1,C,1,1
P101,1728508,1728508,,C,A,GCT,TCT,Non-synonymous,Altering,SAR1660,SAR1660,putative oxygen-independent coproporphyrinogen III oxidase,1,0,0,C,SNP,0,C,1,C,1,1
P101,1732863,1732863,,G,T,AAC,AAA,Non-synonymous,Altering,SAR1664,SAR1664,conserved hypothetical protein,1,0,0,C,SNP,0,G,1,G,1,1
P101,1748655,1748655,,G,C,GCC,GGC,Non-synonymous,Altering,SAR1685,SAR1685,putative biotin carboxylase subunit of acetyl-CoA carboxylase,1,0,0,C,SNP,0,G,1,G,1,1
P101,1769477,1769477,,G,T,CAG,CAT,Non-synonymous,Altering,SAR1707,SAR1707,putative ATPase,0,1,0,D,SNP,0,G,1,G,1,1
P101,1808399,1808399,,C,A,TAG,TAT,Non-synonymous,Altering,SAR1745,SAR1745,putative membrane protein,1,0,0,C,SNP,0,C,1,C,1,1
P101,1835295,1835295,,T,A,TCA,TCT,Synonymous,Silent,SAR1769,SAR1769,DNA polymerase I,1,0,0,C,SNP,0,T,1,T,1,1
P101,1843604,1843604,,T,C,AGT,AGC,Synonymous,Silent,SAR1775,SAR1775,putative D-serine/D-alanine/glycine transporter,1,0,0,C,SNP,0,T,1,T,1,1
P101,1848475,1848475,,C,A,GCT,TCT,Non-synonymous,Altering,SAR1778,SAR1778,acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha,1,0,0,C,SNP,0,C,1,C,1,1
P101,1856091,1856091,,G,A,AGC,AGT,Synonymous,Silent,SAR1783,SAR1783,putative DNA-binding protein,1,0,0,C,SNP,0,A,1,NA,NA,1
P101,1902530,1902530,,G,T,CAT,AAT,Non-synonymous,Altering,SAR1819,SAR1819,FtsK/SpoIIIE family protein,0,1,0,D,SNP,0,G,1,G,1,1
P101,1942969,1942969,,G,A,CAA,TAA,Nonsense,Truncating,SAR1853,SAR1853,bifunctional riboflavin biosynthesis protein,1,0,0,C,SNP,0,G,1,G,1,1
P101,2025155,2025155,,G,T,GCA,GAA,Non-synonymous,Altering,SAR1942,SAR1942,"fumarate hydratase, class-II",1,0,0,C,SNP,0,G,1,G,1,1
P101,2057654,2057654,,G,A,ACT,ATT,Non-synonymous,Altering,SAR1965,SAR1965,ThiJ/PfpI family protein,1,0,0,C,SNP,0,G,1,G,1,1
P101,2086065,2086065,,G,T,ACA,AAA,Non-synonymous,Altering,SAR1996,SAR1996,DNA ligase,1,0,0,C,SNP,0,G,1,G,1,1
P101,2132869,2132869,,G,T,GCT,GAT,Non-synonymous,Altering,SAR2048,SAR2048,hypothetical phage protein,1,0,0,C,SNP,0,G,1,G,1,1
P101,2170968,2170968,,C,A,AGA,ATA,Non-synonymous,Altering,SAR2108,SAR2108,putative leukocidin S subunit,1,0,0,C,SNP,0,C,1,C,1,1
P101,2189275,2189275,,G,A,TAC,TAT,Synonymous,Silent,SAR2128,SAR2128,sucrose-6-phosphate hydrolase,1,0,0,C,SNP,0,G,1,G,1,1
P101,2204093,2204093,,T,C,GTG,GCG,Non-synonymous,Altering,SAR2141,SAR2141,acetolactate synthase large subunit,1,0,0,C,SNP,0,T,1,T,1,1
P101,2234619,2234619,,G,T,TCA,TAA,Nonsense,Truncating,SAR2165,SAR2165,putative potassium-transporting ATPase a chain,0,0,1,B,SNP,0,G,1,G,1,1
P101,2246314,2246314,,T,C,ACT,GCT,Non-synonymous,Altering,SAR2173,SAR2173,hypothetical protein,1,0,0,C,SNP,0,T,1,T,1,1
P101,2299933,2299933,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,C,1,C,1,1
P101,2414781,2414781,,G,T,TTC,TTA,Non-synonymous,Altering,SAR2342,SAR2342,putative membrane protein,1,0,0,C,SNP,0,G,1,G,1,1
P101,2419318,2419318,,C,A,TTG,TTT,Non-synonymous,Altering,SAR2345,SAR2345,AcrB/AcrD/AcrF family protein,0,1,0,D,SNP,0,C,1,C,1,1
P101,2420525,2420525,,C,T,GAT,AAT,Non-synonymous,Altering,SAR2346,SAR2346,putative peptidoglycan pentaglycine interpeptide biosynthesis protein,1,0,0,C,SNP,0,C,1,C,1,1
P101,2429069,2429069,,G,A,CCA,CTA,Non-synonymous,Altering,SAR2357,SAR2357,putative molybdenum cofactor biosynthesis protein,0,0,1,B,SNP,0,G,1,G,1,1
P101,2441680,2441680,,G,A,GCA,ACA,Non-synonymous,Altering,SAR2372,SAR2372,urease gamma subunit,0,0,1,B,SNP,0,G,1,G,1,1
P101,2515537,2515537,,G,T,CCT,ACT,Non-synonymous,Altering,SAR2446,SAR2446,putative permease protein,1,0,0,C,SNP,0,G,1,G,1,1
P101,2581704,2581704,,G,T,GAT,TAT,Non-synonymous,Altering,SAR2508,SAR2508,IgG-binding protein,1,0,0,C,SNP,0,G,1,G,1,1
P101,2593769,2593769,,G,A,CAT,TAT,Non-synonymous,Altering,SAR2518,SAR2518,ABC transporter ATP-binding protein,1,0,0,C,SNP,0,G,1,G,1,1
P101,2612739,2612739,,G,T,GCA,GAA,Non-synonymous,Altering,SAR2533,SAR2533,putative ketopantoate reductase,1,0,0,C,SNP,0,G,1,G,1,1
P101,2680636,2680636,,A,G,GAA,GGA,Non-synonymous,Altering,SAR2595,SAR2595,putative membrane protein,1,0,0,C,SNP,0,A,1,A,1,1
P101,2785876,2785876,,A,C,TCT,GCT,Non-synonymous,Altering,SAR2695,SAR2695,anaerobic ribonucleoside-triphosphate reductase,1,0,0,C,SNP,0,A,1,A,1,1
P101,2815521,2815521,,C,A,CTA,ATA,Non-synonymous,Altering,SAR2719,SAR2719,transcriptional regulator (antiterminator),1,0,0,C,SNP,0,C,1,C,1,1
P101,2840754,2840754,,C,A,AGT,ATT,Non-synonymous,Altering,SAR2734,SAR2734,serine-rich adhesin for platelets,1,0,0,C,SNP,0,C,1,C,1,1
P101,2848868,2848868,,C,A,GGC,GTC,Non-synonymous,Altering,SAR2743,SAR2743,putative capsule synthesis protein,0,1,0,D,SNP,0,C,1,C,1,1
P101,2888048,2888048,,C,A,CAA,AAA,Non-synonymous,Altering,SAR2781,SAR2781,ABC transporter ATP-binding protein,0,1,0,D,SNP,0,C,1,C,1,1
P101,1078788(self),NA,"1171939(MSSA476, BX571857.1)",C,T,GTT,ATT,Non-synonymous,Altering,SAS1099,SAR1139,superantigen-like protein,0,1,0,D,SNP,0,NA,NA,C,1,1
P101,1468119(self),NA,"1556475(MSSA476, BX571857.1)",C,A,GAT,TAT,Non-synonymous,Altering,SAS1429,SAR1563,hypothetical protein,1,0,0,C,SNP,0,NA,NA,C,1,1
P101,2434532(self),NA,"2559544(MSSA476, BX571857.1)",A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,G,1,1
P101,261935(self),NA,"317666(MSSA476, BX571857.1)",G,T,AAG,AAT,Non-synonymous,Altering,SAS0268,(no ortholog),hypothetical protein,1,0,0,C,SNP,0,NA,NA,G,1,1
P101,382342(self),NA,"442603(MSSA476, BX571857.1)",G,A,GAA,AAA,Non-synonymous,Altering,SAS0396,SAR0435,exotoxin,1,0,0,C,SNP,0,NA,NA,A,1,1
P101,k31_var_103,858910,,A,AA,GTG,AGT,"Frameshift, stop gained",Truncating,SAR0815,SAR0815,prolipoprotein diacylglyceryl transferase,1,0,0,C,ShINDEL,1,NA,NA,AA,1,1
P101,k31_var_118,NA,"1764269(MSSA476, BX571857.1)",A,G,ACT,GCT,Non-synonymous,Altering,SAS1632,SAR1783,putative DNA-binding protein,1,0,0,C,SNP,0,NA,NA,A,1,1
P101,k31_var_121,196535,,A,AT,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,AT,1,1
P101,k31_var_59,2697692,,CT,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,CT,1,1
P101,k31_var_70,1199607,,ATTAAAA,A,ATT,AAA,"Non-synonymous, 2 codon deletion",Altering,SAR1157,SAR1157,penicillin-binding protein 1,1,0,0,C,ShINDEL,6,NA,NA,ATTAAAA,1,1
P101,k31_var_82,NA,"420984(ED98, NC_013450.1)",A,C,ATG,CTG,Non-synonymous,Altering,SAAV_0382,(no ortholog),putative lipoprotein,1,0,0,C,SNP,0,NA,NA,C,1,1
P101,k31_var_83,2503672,,AT,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,AT,1,1
P101,k61_var_119,907284,,C,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,NA,NA,C,1,1
P101,k61_var_81,2034098,,TACACCTATACCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTCCCGCATCATTATTAAATTATGGAGCGGAAGATAGGATTT,T,NA,NA,"Non-synonymous, 30 codon deletion",Altering,SAR_RS10035,SARt027,tRNA-Gly,1,0,0,C,ShINDEL,90,NA,NA,TACACCTATACCTCGTTCCGGGAAGGAACGTGTTCTAAAAGTTGAACTACTCCCGCATCATTATTAAATTATGGAGCGGAAGATAGGATTT,1,1
P103,774701,774701,,G,T,CAA,AAA,Non-synonymous,Altering,SAR0739,SAR0739,MarR family regulatory protein,0,0,1,B,SNP,0,G,1,G,1,1
P103,845406,845406,,T,C,GTA,GCA,Non-synonymous,Altering,SAR0807,SAR0807,preprotein translocase SecA subunit,0,0,1,B,SNP,0,T,0,T,0,0
P103,1195956,1195956,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P103,1350970,1350970,,G,T,AGA,ATA,Non-synonymous,Altering,SAR1285,SAR1285,hypothetical protein,0,0,1,B,SNP,0,G,1,G,1,1
P103,1569701,1569701,,T,C,CCA,CCG,Synonymous,Silent,SAR1475,SAR1475,3-phosphoshikimate 1-carboxyvinyltransferase,0,0,1,B,SNP,0,T,1,T,1,1
P103,1692321,1692321,,C,T,GGA,GAA,Non-synonymous,Altering,SAR1622,SAR1622,metallo-beta-lactamase superfamily protein,0,0,1,B,SNP,0,C,1,C,1,1
P103,2566589,2566589,,C,T,GAA,AAA,Non-synonymous,Altering,SAR2491,SAR2491,acetyltransferase (GNAT) family protein,0,0,1,B,SNP,0,C,1,C,1,1
P103,2755951,2755951,,G,A,GCG,ACG,Non-synonymous,Altering,SAR2669,SAR2669,putative dihydroorotate dehydrogenase,0,0,1,B,SNP,0,G,0,G,0,0
P103,2899235,2899235,,T,C,ACG,GCG,Non-synonymous,Altering,SAR2797,SAR2797,glucose inhibited division protein A,0,0,1,B,SNP,0,T,1,T,1,1
P103,k31_var_140,2811729,,CCC,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,2,NA,NA,C,0,0
P103,k31_var_144,1461601,,A,AA,ATG,TGG,"Frameshift, stop gained",Truncating,SAR1404,SAR1404,ABC transporter ATP-binding protein,0,0,1,B,ShINDEL,1,NA,NA,AA,0,0
P103,k31_var_146,2357509,,AT,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,AT,1,1
P103,k31_var_150,2339344,,G,GT,TAC,TAA,Nonsense,Truncating,SAR_RS11790,(no ortholog),multidrug MFS transporter,0,0,1,B,ShINDEL,1,NA,NA,G,1,1
P103,k31_var_54,2573125,,TA,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,T,1,1
P104,243459,243459,,G,A,ACG,ACA,Synonymous,Silent,SAR0209,SAR0209,putative oxidoreductase,1,0,0,C,SNP,0,G,1,G,1,1
P104,1932689,1932689,,C,A,GAT,TAT,Non-synonymous,Altering,SAR1843,SAR1843,leucyl-tRNA synthetase,1,0,0,C,SNP,0,C,1,C,1,1
P104,2581425,2581425,,C,T,CAC,TAC,Non-synonymous,Altering,SAR2508,SAR2508,IgG-binding protein,1,0,0,C,SNP,0,C,1,C,1,1
P104,k61_var_1113,NA,"1244204(MSSA476, BX571857.1)",TATAAGAAACACTAATCAATAAATTGATAAGAAGATTAGAGGAACGCCTGAGCTAAAGCTCATGC,T,TTA,TTC,"Frameshift, stop gained",Truncating,SAS_RS06185,(no ortholog),hypothetical protein,0,0,1,B,ShINDEL,64,NA,NA,TATAAGAAACACTAATCAATAAATTGATAAGAAGATTAGAGGAACGCCTGAGCTAAAGCTCATGC,1,1
P105,167706,167706,,A,C,GAA,GCA,Non-synonymous,Altering,SAR0150,SAR0150,putative aldehyde-alcohol dehydrogenase,1,0,0,C,SNP,0,A,1,A,1,1
P105,318424,318424,,T,C,TAC,CAC,Non-synonymous,Altering,SAR0273,SAR0273,peptidoglycan hydrolase,1,0,0,C,SNP,0,T,1,T,1,1
P105,379208,379208,,G,T,ACA,AAA,Non-synonymous,Altering,SAR0333,SAR0333,putative glycerol-3-phosphate transporter,1,0,0,C,SNP,0,G,1,G,1,1
P105,838617,838617,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,0,A,0,0
P105,1114771,1114771,,C,T,GCT,GTT,Non-synonymous,Altering,SAR1068,SAR1068,"putative pyruvate dehydrogenase E1 component, beta subunit",0,0,1,B,SNP,0,C,0,C,0,0
P105,1396905,1396905,,A,T,GAT,GTT,Non-synonymous,Altering,SAR1347,SAR1347,putative GMP reductase,1,0,0,C,SNP,0,A,1,A,1,1
P105,1482499,1482499,,C,G,GCA,CCA,Non-synonymous,Altering,SAR1424,SAR1424,dihydrolipoamide succinyltransferase E2 component of 2-oxoglutarate dehydrogenase complex,1,0,0,C,SNP,0,C,1,C,1,1
P105,1953016,1953016,,A,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,A,0,NA,NA,0
P105,2193770,2193770,,T,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,SNP,0,T,1,T,1,1
P105,2321186,2321186,,C,A,GCC,GCT,Synonymous,Silent,SAR2248,SAR2248,putative surface anchored protein (pseudogene),0,1,0,D,SNP,0,C,1,C,1,1
P105,2686234,2686234,,T,C,TAT,TGT,Non-synonymous,Altering,SAR2599,SAR2599,putative dioxygenase,1,0,0,C,SNP,0,T,1,T,1,1
P105,1128134(self),NA,unknown,C,T,GAA,AAA,Non-synonymous,Altering,SAR1562,SAR1562,phage integrase,0,0,1,B,SNP,0,NA,NA,C,1,1
P105,142411(self),NA,unknown,A,C,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,SNP,0,NA,NA,NA,NA,NA
P105,2425175(self),2736518,,G,A,AAT,AAC,Synonymous,Silent,SAR2648,SAR2648,secretory antigen precursor,1,0,0,C,SNP,0,NA,NA,G,1,1
P105,660075(self),NA,unknown,G,A,CGT,CAT,Non-synonymous,Altering,SAAV_c04,(no ortholog),putative resolvase,1,0,0,C,SNP,0,NA,NA,NA,NA,NA
P105,k31_var_106,NA,"1853988(MSSA476, BX571857.1)",G,GA,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,1,NA,NA,GA,0,0
P105,k31_var_113,2219992,,T,TGA,CAT,CCT,"Frameshift, stop gained",Truncating,SAR2150,SAR2150,YP_041512.1,0,0,1,B,ShINDEL,2,NA,NA,T,1,1
P105,k31_var_42,NA,"24582(MSSA476, BX571857.1)",GACGAATA,G,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,7,NA,NA,GACGAATA,1,1
P105,k31_var_97,NA,"2356064(MSSA476, BX571857.1)",TAT,T,NA,NA,Intergenic,Intergenic,NA,NA,NA,0,0,1,B,ShINDEL,2,NA,NA,T,0,0
P105,k61_var_16,NA,"2083799(MSSA476, BX571857.1)",G,GTCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCTGGATTTGGTTTCGGGTTATCTGGA,GAC,GTC,Non-synonymous plus 26 codon insertion,Altering,SAS1938,SAR2119,membrane anchored protein,1,0,0,C,ShINDEL,78,NA,NA,GTCTGGTTTTGGATCCGGATTTGGCTTTGGTTTATCTGGGTCTGGTTTTGGATCTGGATTTGGTTTCGGGTTATCTGGA,1,1
P105,k61_var_26,NA,"5614(plasmid pUSA300HOUMS, NC_010066.1)",AA,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,NA,NA,NA
P105,k61_var_51,NA,"9231(plasmid pUSA300HOUMS, NC_010066.1)",AT,A,NA,NA,Intergenic,Intergenic,NA,NA,NA,1,0,0,C,ShINDEL,1,NA,NA,NA,NA,NA