Table 1.
Characterization of the genetic heterogeneity Sites and SNP in large gene families
| Maq | Chrom Position | Genotype profile at selected loci of SRX007711 | Genotype profile at selected loci of FPR3757 | Read Depth | SRX007711 Mean Phred Values | Max Phred Value | Functional Description |
|---|---|---|---|---|---|---|---|
| I. Heterogeneity sites that passed the SNPfilter and have an average of per-base Phred value greater than 13 | |||||||
| * | 778416 | T:6 G:140 | G:37 | 6 | 31.5 | 40 | sulfatase family protein |
| * | 2512836 | C:7 G:115 | G:37 | 8 | 31.25 | 40 | sensor histidine kinase |
| * | 107624 | A:5 C:110 | C:37 | 5 | 29.8 | 40 | hypothetical protein |
| * | 435033 | T:5 G:98 | G:37 | 5 | 28.2 | 38 | hypothetical protein |
| * | 1021087 | T:5 G:151 | G:37 | 5 | 26.2 | 40 | lipoate-protein ligase A family protein |
| * | 1662849 | A:5 C:134 | C:37 | 6 | 24.66 | 40 | penicillin-binding protein 3 |
| * | 2648343 | A:5 C:192 | C:37 | 5 | 24.6 | 40 | drug transporter phosphotransferase system, glucose- |
| * | 2674216 | A:5 C:170 | C:37 | 5 | 24.6 | 40 | specific IIABC component |
| * | 1542366 | T:6 G:129 | G:37 | 6 | 24.5 | 40 | hypothetical protein lantibiotic epidermin biosynthesis |
| * | 1950547 | A:5 C:164 | C:37 | 5 | 23.4 | 40 | protein EpiC |
| * | 105211 | A:6 G:132 | G:37 | 8 | 20.3 | 40 | hypothetical protein |
| * | 1857182 | A:14 G:85 | G:37 | 14 | 19.42 | 40 | hypothetical protein phiSLT ORF2067-like protein, phage |
| * | 1558524 | T:5 G:56 | G:37 | 7 | 17.57 | 40 | tail tape measure protein phi77 ORF014-like protein, phage anti- |
| * | 2122182 | C:122 G:6 | C:37 | 6 | 17.28 | 38 | repressor protein |
| * | 1383603 | A:5 G:128 | G:37 | 5 | 15.8 | 20 | oxacillin resistance-related FmtC protein |
| (A:2) T:5 | lactose phosphotransferase system | ||||||
| * | 2333470 | C:164 | C:37 | 7 | 15.28 | 40 | repressor |
| putative fibronectin/fibrinogen binding | |||||||
| * | 1206348 | A:1 T:6 G:145 | G:37 | 7 | 14.71 | 25 | protein |
| A:153 (T:1) | |||||||
| * | 2262790 | G:6 | A:37 | 7 | 13.14 | 29 | cation efflux family protein |
| II. Heterogeneity sites that did not pass the SNPfilter but have an average per base Phred value greater than 13 | |||||||
| 1180638 | T:5 G:97 | G:37 | 5 | 40 | 40 | cell division protein ftsA | |
| 2-oxoglutarate dehydrogenase E1 | |||||||
| 1437922 | C:149 G:5 | C:37 | 5 | 39.2 | 40 | component | |
| 2212436 | A:5 C:107 | C:37 | 5 | 37.8 | 40 | thiamine-phosphate pyrophosphorylase | |
| 257712 | T:5 G:101 | G:37 | 5 | 35.6 | 40 | sensor histidine kinase family protein | |
| 861340 | A:9 C:136 | C:49 | 10 | 34 | 40 | clumping factor A | |
| acetyl-CoA carboxylase, biotin carboxyl | |||||||
| 1714319 | T:6 C:95 | C:37 | 6 | 34 | 40 | carrier protein | |
| 1252956 | T:9 G:125 | G:37 | 9 | 33 | 40 | DNA topoisomerase I | |
| lantibiotic epidermin leader peptide | |||||||
| 1948255 | A:5 C:169 | C:37 | 5 | 32.8 | 40 | processing serine protease EpiP | |
| 955972 | A:5 C:145 | C:37 | 5 | 32.6 | 40 | Hypothetical protein | |
| 2123183 | A:25 X:29 | A:37 | 29 | 31.44 | 40 | putative phage transcriptional regulator | |
| 2638027 | A:5 C:112 | C:36 | 5 | 31 | 40 | gluconate kinase | |
| 1829558 | T:5 G:118 | G:37 | 5 | 30.8 | 40 | septation ring formation regulator EzrA | |
| putative maltose ABC transporter, | |||||||
| 247386 | A:5 C:163 | C:37 | 5 | 30.4 | 40 | maltose-binding protein | |
| 2262622 | C:5 G:156 | G:37 | 5 | 30.4 | 40 | cation efflux family protein | |
| 344352 | C:460 G:7 | C:131 | 8 | 29.5 | 40 | Hypothetical protein | |
| 346978 | C:383 G:7 | C:113 | 8 | 29.5 | 40 | Hypothetical protein | |
| 472492 | T:5 G:194 | G:37 | 5 | 29.4 | 40 | Hypothetical protein | |
| 2175831 | A:585 G:8 | A:229 | 9 | 28 | 40 | 5 S ribosomal RNA | |
| 1753468 | C:96 G:5 | C:37 | 5 | 27.2 | 40 | Hypothetical protein | |
| 1503664 | A:113 T:6 | A:37 | 6 | 27.16 | 40 | Hypothetical protein | |
| 617974 | A:374 T:5 | A:99 | 5 | 26.2 | 38 | sdrD protein | |
| 154794 | A:5 C:136 | C:37 | 5 | 25.6 | 40 | Fe/Mn family superoxide dismutase | |
| 1943616 | C:5 G:110 | G:37 | 5 | 25.2 | 32 | serine protease SplA | |
| 2064321 | C:113 G:6 | C:37 | 6 | 24.8 | 40 | Hypothetical protein | |
| 910508 | A:177 T:6 | A:37 | 7 | 24 | 40 | lipoyl synthase | |
| 5-methyltetrahydropteroyltriglutamate-- | |||||||
| 408863 | T:6 G:160 | G:37 | 6 | 23.16 | 40 | homocysteine S-methyltransferase | |
| 2417570 | A:5 G:109 | G:37 | 5 | 22.8 | 39 | Na+/H+ antiporter NhaC | |
| glycerol uptake operon antiterminator | |||||||
| 1311574 | A:5 C:181 | C:37 | 5 | 22.6 | 40 | regulatory protein | |
| capsular polysaccharide biosynthesis | |||||||
| 175115 | X:6 G:136 | G:37 | 6 | 21.33 | 40 | protein Cap5B | |
| 2775087 | A:14 T:107 | T:49 | 14 | 20.4 | 29 | clumping factor B | |
| 2678195 | A:5 G:92 | G:37 | 5 | 19.4 | 27 | LysR family transcriptional regulator | |
| 451366 | C:5 G:119 | G:37 | 5 | 19.2 | 33 | Superantigen-like protein 5 | |
| 1633215 | A:5 C:83 | C:37 | 5 | 18.4 | 28 | putative traG membrane protein | |
| 2114835 | A:6 C:136 | C:37 | 7 | 17.14 | 27 | phiPVL ORF046-like protein | |
| 1859648 | C:5 X:1 G:121 | G:37 | 6 | 16 | 24 | FtsK/SpoIIIE family protein | |
| 467549 | A:89 T:23 | A:58 | 23 | 15.56 | 40 | Staphylococcal tandem lipoprotein | |
| 2123177 | A:57 X:5 | A:37 | 5 | 15.4 | 21 | putative phage transcriptional regulator | |
| 36501 | A:29 G:391 | G:192 | 29 | 15.13 | 40 | putative transposase | |
| 1857109 | A:162 G:12 | A:37 | 12 | 14 | 40 | hypothetical protein | |
| 950365 | A:5 C:113 | C:37 | 5 | 13.8 | 17 | Exonuclease RexB | |
| 801123 | T:5 G:91 | G:37 | 5 | 13.4 | 28 | transferrin receptor | |
| 2481059 | T:5 G:148 | G:37 | 5 | 13.4 | 21 | response regulator protein | |
| 1545118 | A:15 T:109 | T:37 | 15 | 13.2 | 40 | putative lipoprotein | |
| IV. Heterogeneity sites at RNA genes that pass the SNPfileter when single RNA genes were used as reference sequence. | |||||||
| * | 1997102 | A:69 T:13 | A:37 | 13 | 7.0 | 30 | Leu tRNA |
| 1996261 | T:7 C:76 | C:55 | 8 | 14.25 | 30 | Met tRNA | |
| * | 1961354 | T:12 C:25 | C:55 | 12 | 20.16 | 40 | Met tRNA |
| 517898 | T:581 C:8 | T:231 | 8 | 31.37 | 40 | 5 S ribosomal RNA | |
| * | 556291 | T:560 C:16 | T:225 | 16 | 20.56 | 40 | 5 S ribosomal RNA |
| 561501 | T:580 C:8 | T:229 | 8 | 31.37 | 40 | 5 S ribosomal RNA | |
| 1997607 | A:569 G:8 | A:218 | 8 | 31.37 | 40 | 5 S ribosomal RNA | |
| 2292385 | A:549 G:8 | A:218 | 8 | 31.37 | 40 | 5 S ribosomal RNA | |
| 516288 | A:34 G:408 | G:185 | 34 | 14.11 | 40 | 23 S ribosomal RNA | |
| 517172 | T:6 G:495 | G:185 | 6 | 13.83 | 26 | 23 S ribosomal RNA | |
| 559891 | A:34 G:408 | G:185 | 34 | 14.1 | 40 | 23 S ribosomal RNA | |
| 560775 | T:6 G:495 | G:185 | 6 | 13.83 | 26 | 23 S ribosomal RNA | |
| 1998333 | A:6 C:495 | C:185 | 6 | 13.8 | 26 | 23 S ribosomal RNA | |
| 1999217 | T:34 C:408 | C:185 | 34 | 14.11 | 40 | 23 S ribosomal RNA | |
| 2176557 | A:6 C:495 | C:185 | 6 | 13.83 | 26 | 23 S ribosomal RNA | |
| 2177441 | T:34 C:408 | C:185 | 34 | 14.1 | 40 | 23 S ribosomal RNA | |
| 2293111 | A:6 C:495 | C:185 | 6 | 13.83 | 26 | 23 S ribosomal RNA | |