"Supplementary Data File 3: Location and annotation of single nucleotide polymorphisms (SNPs) across the mitogenome of the Atlantic Puffin detected by sequencing 71 individuals across 12 colonies. Genotypes were jointly called with GATK v4.1.4 by using the HaplotypeCaller, CombineGVCFs and GenotypeGVCFs tool. Genotypes were filtered with BCFtools v1.9 according to GATKs Best Practices. Indels and non-biallelic SNPs were removed and only SNPs present in all individuals were kept. ",,,,,,,
Position,Reference,Alternate,Annotation,Gene Name,Amino Acid Change,,
56,T,C,non_coding_transcript_variant,trnF,,,
209,A,G,non_coding_transcript_variant,rrnS,,,
241,C,T,non_coding_transcript_variant,rrnS,,,
342,A,G,non_coding_transcript_variant,rrnS,,,
437,T,C,non_coding_transcript_variant,rrnS,,,
500,C,T,non_coding_transcript_variant,rrnS,,,
857,C,T,non_coding_transcript_variant,rrnS,,,
888,T,C,non_coding_transcript_variant,rrnS,,,
963,C,T,non_coding_transcript_variant,rrnS,,,
979,C,T,non_coding_transcript_variant,rrnS,,,
1128,A,G,non_coding_transcript_variant,rrnL,,,
1247,C,T,non_coding_transcript_variant,rrnL,,,
1511,C,T,non_coding_transcript_variant,rrnL,,,
1850,T,C,non_coding_transcript_variant,rrnL,,,
2268,G,A,non_coding_transcript_variant,rrnL,,,
2285,C,T,non_coding_transcript_variant,rrnL,,,
2303,G,A,non_coding_transcript_variant,rrnL,,,
2480,T,C,non_coding_transcript_variant,rrnL,,,
2583,A,G,non_coding_transcript_variant,rrnL,,,
2657,T,C,non_coding_transcript_variant,rrnL,,,
3273,A,G,missense_variant,nad1,p.Ile161Val,,
3284,C,T,synonymous_variant,nad1,p.Ser164Ser,,
3317,C,T,synonymous_variant,nad1,p.Thr175Thr,,
3323,G,A,synonymous_variant,nad1,p.Glu177Glu,,
3416,G,A,synonymous_variant,nad1,p.Thr208Thr,,
3599,A,G,synonymous_variant,nad1,p.Lys269Lys,,
3618,G,A,missense_variant,nad1,p.Gly276Ser,,
3849,A,G,intergenic_region,trnI-trnQ,,,
4044,A,G,missense_variant,nad2,p.Ile19Val,,
4115,C,A,synonymous_variant,nad2,p.Pro42Pro,,
4274,C,T,synonymous_variant,nad2,p.Cys95Cys,,
4418,C,T,synonymous_variant,nad2,p.Phe143Phe,,
4472,A,C,synonymous_variant,nad2,p.Ser161Ser,,
4491,A,G,missense_variant,nad2,p.Met168Val,,
4550,G,A,synonymous_variant,nad2,p.Leu187Leu,,
4559,G,A,synonymous_variant,nad2,p.Met190Met,,
4573,T,C,missense_variant,nad2,p.Ile195Thr,,
4608,A,G,missense_variant,nad2,p.Ile207Val,,
4760,C,T,synonymous_variant,nad2,p.Leu257Leu,,
4788,A,G,missense_variant,nad2,p.Ile267Val,,
5187,C,T,non_coding_transcript_variant,trnN,,,
5483,C,T,synonymous_variant,cox1,p.Thr32Thr,,
5700,C,T,synonymous_variant,cox1,p.Leu105Leu,,
5702,A,G,synonymous_variant,cox1,p.Leu105Leu,,
5723,G,A,synonymous_variant,cox1,p.Leu112Leu,,
5753,A,G,synonymous_variant,cox1,p.Gly122Gly,,
5759,T,C,synonymous_variant,cox1,p.Gly124Gly,,
5804,C,T,synonymous_variant,cox1,p.His139His,,
5972,A,G,synonymous_variant,cox1,p.Leu195Leu,,
5996,C,T,synonymous_variant,cox1,p.Leu203Leu,,
5999,T,C,synonymous_variant,cox1,p.Ala204Ala,,
6035,A,G,synonymous_variant,cox1,p.Leu216Leu,,
6146,G,A,synonymous_variant,cox1,p.Gly253Gly,,
6221,G,A,synonymous_variant,cox1,p.Met278Met,,
6222,C,T,synonymous_variant,cox1,p.Leu279Leu,,
6242,A,G,synonymous_variant,cox1,p.Gly285Gly,,
6299,T,G,synonymous_variant,cox1,p.Ala304Ala,,
6326,T,C,synonymous_variant,cox1,p.Ile313Ile,,
6362,C,T,synonymous_variant,cox1,p.Leu325Leu,,
6569,T,C,synonymous_variant,cox1,p.Phe394Phe,,
6585,T,C,synonymous_variant,cox1,p.Leu400Leu,,
6674,G,A,synonymous_variant,cox1,p.Gln429Gln,,
6836,A,T,synonymous_variant,cox1,p.Val483Val,,
6891,C,T,missense_variant,cox1,p.Pro502Ser,,
6990,C,T,non_coding_transcript_variant,trnS2,,,
7222,A,G,synonymous_variant,cox2,p.Lys49Lys,,
7300,T,C,synonymous_variant,cox2,p.Leu75Leu,,
7440,T,C,missense_variant,cox2,p.Ile122Thr,,
7453,G,A,synonymous_variant,cox2,p.Glu126Glu,,
7499,G,A,missense_variant,cox2,p.Val142Ile,,
7525,C,T,synonymous_variant,cox2,p.Arg150Arg,,
7543,C,T,synonymous_variant,cox2,p.Asp156Asp,,
7564,T,C,synonymous_variant,cox2,p.Ala163Ala,,
7579,G,A,synonymous_variant,cox2,p.Gly168Gly,,
7606,A,G,synonymous_variant,cox2,p.Arg177Arg,,
7939,G,A,synonymous_variant,atp8,p.Leu36Leu,,
7965,T,C,missense_variant,atp8,p.Ile45Thr,,
8026,T,C,missense_variant,atp6,p.Tyr13His,,
8067,T,C,synonymous_variant,atp6,p.Phe26Phe,,
8289,C,T,synonymous_variant,atp6,p.Ser100Ser,,
8309,T,C,missense_variant,atp6,p.Phe107Ser,,
8370,C,T,synonymous_variant,atp6,p.Gly127Gly,,
8546,T,C,missense_variant,atp6,p.Ile186Thr,,
8622,G,A,synonymous_variant,atp6,p.Gln211Gln,,
8738,C,T,synonymous_variant,cox3,p.Ala22Ala,,
8765,A,G,synonymous_variant,cox3,p.Leu31Leu,,
8813,G,A,synonymous_variant,cox3,p.Leu47Leu,,
9026,T,C,synonymous_variant,cox3,p.Pro118Pro,,
9041,C,T,synonymous_variant,cox3,p.Pro123Pro,,
9096,G,A,missense_variant,cox3,p.Val142Ile,,
9113,G,A,synonymous_variant,cox3,p.Ala147Ala,,
9170,G,A,synonymous_variant,cox3,p.Thr166Thr,,
9254,G,A,synonymous_variant,cox3,p.Gly194Gly,,
9294,G,A,missense_variant,cox3,p.Val208Ile,,
9320,G,A,synonymous_variant,cox3,p.Ser216Ser,,
9615,G,A,synonymous_variant,nad3,p.Pro25Pro,,
9627,G,A,synonymous_variant,nad3,p.Lys29Lys,,
9874,A,G,splice_region_variant&synonymous_variant,nad3,p.???112???,,
10004,T,C,synonymous_variant,nad4l,p.Leu19Leu,,
10017,G,A,missense_variant,nad4l,p.Arg23Gln,,
10045,C,T,synonymous_variant,nad4l,p.Cys32Cys,,
10468,A,G,missense_variant,nad4,p.Met77Val,,
10500,G,A,synonymous_variant,nad4,p.Glu87Glu,,
10506,G,A,synonymous_variant,nad4,p.Leu89Leu,,
10507,A,G,missense_variant,nad4,p.Thr90Ala,,
10528,C,A,missense_variant,nad4,p.Leu97Met,,
10716,G,A,synonymous_variant,nad4,p.Pro159Pro,,
10726,G,A,missense_variant,nad4,p.Ala163Thr,,
10737,T,C,synonymous_variant,nad4,p.Tyr166Tyr,,
10744,A,G,missense_variant,nad4,p.Thr169Ala,,
10824,G,A,synonymous_variant,nad4,p.Ser195Ser,,
11079,T,C,synonymous_variant,nad4,p.Thr280Thr,,
11082,T,C,synonymous_variant,nad4,p.Asp281Asp,,
11223,T,C,synonymous_variant,nad4,p.Cys328Cys,,
11224,C,T,synonymous_variant,nad4,p.Leu329Leu,,
11247,T,C,synonymous_variant,nad4,p.Arg336Arg,,
11337,T,C,synonymous_variant,nad4,p.Asn366Asn,,
11448,T,C,synonymous_variant,nad4,p.Thr403Thr,,
11460,C,T,synonymous_variant,nad4,p.Thr407Thr,,
11509,G,A,missense_variant,nad4,p.Ala424Thr,,
11511,A,G,synonymous_variant,nad4,p.Ala424Ala,,
11697,T,C,non_coding_transcript_variant,trnS1,,,
11829,G,A,missense_variant,nad5,p.Ala10Thr,,
11831,T,C,synonymous_variant,nad5,p.Ala10Ala,,
11964,G,A,missense_variant,nad5,p.Ala55Thr,,
11978,G,A,synonymous_variant,nad5,p.Pro59Pro,,
12008,G,A,synonymous_variant,nad5,p.Glu69Glu,,
12058,C,T,missense_variant,nad5,p.Pro86Leu,,
12060,G,A,missense_variant,nad5,p.Val87Ile,,
12086,G,A,synonymous_variant,nad5,p.Ser95Ser,,
12110,A,T,synonymous_variant,nad5,p.Leu103Leu,,
12237,C,A,missense_variant,nad5,p.Leu146Met,,
12315,G,A,missense_variant,nad5,p.Glu172Lys,,
12320,C,T,synonymous_variant,nad5,p.Ala173Ala,,
12368,T,C,synonymous_variant,nad5,p.Ile189Ile,,
12527,C,T,synonymous_variant,nad5,p.Pro242Pro,,
12784,A,G,missense_variant,nad5,p.Asn328Ser,,
12798,G,A,missense_variant,nad5,p.Ala333Thr,,
12839,G,A,synonymous_variant,nad5,p.Met346Met,,
12857,A,G,synonymous_variant,nad5,p.Gly352Gly,,
12869,C,T,synonymous_variant,nad5,p.His356His,,
12881,A,C,synonymous_variant,nad5,p.Gly360Gly,,
12960,G,A,missense_variant,nad5,p.Ala387Thr,,
12973,C,T,missense_variant,nad5,p.Thr391Ile,,
13070,T,C,synonymous_variant,nad5,p.Ala423Ala,,
13170,G,A,missense_variant,nad5,p.Ala457Thr,,
13256,C,A,synonymous_variant,nad5,p.Thr485Thr,,
13302,G,A,missense_variant,nad5,p.Val501Ile,,
13529,C,T,synonymous_variant,nad5,p.Asp576Asp,,
13664,T,C,missense_variant,cob_0,p.Phe5Ser,,
13674,C,T,synonymous_variant,cob_0,p.Ser8Ser,,
13719,C,T,synonymous_variant,cob_0,p.Pro23Pro,,
13968,T,C,synonymous_variant,cob_0,p.Gly106Gly,,
14001,C,T,synonymous_variant,cob_0,p.Gly117Gly,,
14052,G,A,synonymous_variant,cob_0,p.Leu134Leu,,
14244,T,C,synonymous_variant,cob_0,p.Leu198Leu,,
14298,C,T,synonymous_variant,cob_0,p.Cys216Cys,,
14346,G,A,synonymous_variant,cob_0,p.Gly232Gly,,
14354,T,C,missense_variant,cob_0,p.Ile235Thr,,
14385,A,G,synonymous_variant,cob_0,p.Leu245Leu,,
14440,G,A,missense_variant,cob_0,p.Val264Ile,,
14552,T,C,missense_variant,cob_0,p.Val301Ala,,
14571,G,A,synonymous_variant,cob_0,p.Leu307Leu,,
14593,G,A,missense_variant,cob_0,p.Ala315Thr,,
14609,C,T,missense_variant,cob_0,p.Pro320Leu,,
14641,G,A,missense_variant,cob_0,p.Ala331Thr,,
14751,C,T,synonymous_variant,cob_0,p.Phe367Phe,,
14790,C,T,synonymous_variant,cob_0,p.Tyr380Tyr,,
14810,T,C,non_coding_transcript_variant,trnT,,,
14866,T,C,intergenic_region,trnT-trnP,,,
14969,G,A,synonymous_variant,nad6,p.Ala169Ala,,
14989,G,A,missense_variant,nad6,p.Arg163Cys,,
15038,T,C,synonymous_variant,nad6,p.Val146Val,,
15039,A,C,missense_variant,nad6,p.Val146Gly,,
15041,T,C,synonymous_variant,nad6,p.Leu145Leu,,
15164,G,A,synonymous_variant,nad6,p.Val104Val,,
15166,C,T,missense_variant,nad6,p.Val104Ile,,
15172,A,G,synonymous_variant,nad6,p.Leu102Leu,,
15176,C,T,synonymous_variant,nad6,p.Met100Met,,
15200,C,T,synonymous_variant,nad6,p.Val92Val,,
15203,C,T,synonymous_variant,nad6,p.Gly91Gly,,
15251,C,T,synonymous_variant,nad6,p.Ala75Ala,,
15293,T,C,synonymous_variant,nad6,p.Gly61Gly,,
15323,T,C,synonymous_variant,nad6,p.Val51Val,,
15332,G,A,synonymous_variant,nad6,p.Val48Val,,
15435,A,C,missense_variant,nad6,p.Leu14Trp,,
15713,C,T,intergenic_region,Control Region,,,
15728,A,G,intergenic_region,Control Region,,,
15797,C,T,intergenic_region,Control Region,,,
15858,T,C,intergenic_region,Control Region,,,
16034,G,A,intergenic_region,Control Region,,,
16366,A,G,intergenic_region,Control Region,,,