Table 1 Target regions used in this study and the number of validated SNPs
From: Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing
Region | Region size including primer binding sites (bp) | Amplicon number | Amplicon size excluding primer binding sites (bp) | Number of SNPs | SNPs per base-1 | Average number of reads supporting the SNPs per individual | Multiallelic SNPs | Transitions | Transversion | Indels |
|---|---|---|---|---|---|---|---|---|---|---|
DLOOPB | 423 | 1 | 381 | 21 | 0,055118 | 25.4 (±10.3) | 1 | 11 | 8 | 2 |
ND1 | 1161 | 2 | 384 | 15 | 0,039063 | 28.0 (±16.3) | 1 | 13 | 2 |  |
|  |  | 3 | 369 | 5 | 0,013550 | 28.2 (±12.3) |  | 5 |  |  |
|  |  | 4 | 324 | 8 | 0,024691 | 13.9 (±5.8) |  | 8 |  |  |
ND2 | 770 | 5 | 361 | 13 | 0,036011 | 34.1 (±11.7) |  | 13 |  |  |
|  |  | 6 | 346 | 7 | 0,020231 | 29.1 (±17.1) |  | 5 | 2 |  |
COXI | 821 | 7 | 372 | 12 | 0,032258 | 21.2 (±11.6) |  | 12 |  |  |
|  |  | 8 | 382 | 12 | 0,031414 | 40.9 (±14.2) |  | 11 | 1 |  |
COXII | 715 | 9 | 361 | 7 | 0,019391 | 48.0 (±19.3) |  | 7 |  |  |
|  |  | 10 | 311 | 7 | 0,022508 | 17.3 (±7.6) |  | 7 |  |  |
ATP6 | 414 | 11 | 375 | 13 | 0,034667 | 35.9 (±14.1) |  | 11 | 2 |  |
ND3 | 403 | 12 | 357 | 10 | 0,028011 | 30.5 (±12.8) |  | 9 | 1 |  |
ND4 | 1181 | 13 | 363 | 12 | 0,033058 | 27.6 (±11.6) |  | 12 |  |  |
|  |  | 14 | 361 | 13 | 0,036011 | 26.7 (±12.5) |  | 13 |  |  |
|  |  | 15 | 370 | 13 | 0,035135 | 19.3 (±9.8) |  | 12 | 1 |  |
ND5 | 783 | 16 | 345 | 8 | 0,023188 | 21.3 (±8.4) |  | 8 |  |  |
|  |  | 17 | 370 | 12 | 0,032432 | 20.5 (±8.5) |  | 12 |  |  |
CYTB | 1161 | 18 | 366 | 10 | 0,027322 | 35.9 (±14.6) |  | 10 |  |  |
|  |  | 19 | 352 | 8 | 0,022727 | 14.5 (±6.2) |  | 8 |  |  |
|  |  | 20 | 365 | 12 | 0,032877 | 25.6 (±9.9) | 1 | 9 | 3 |  |
Totals | 7832 |  | 7215 | 218 | 0,030215 | 27.3 (±11.7) | 3 | 196 | 20 | 2 |