Table 1.
Counts of variants per chromosome
| Chromosome | Biallelic | Triallelic | InDels |
|---|---|---|---|
| 1 |
953,116 |
1,594 |
106,808 |
| 2 |
765,523 |
1,540 |
86,271 |
| 3 |
689,653 |
1,061 |
74,819 |
| 4 |
727,730 |
1,059 |
81,188 |
| 5 |
711,291 |
1,236 |
78,518 |
| 6 |
715,956 |
1,306 |
81,170 |
| 7 |
647,618 |
944 |
72,861 |
| 8 |
662,730 |
929 |
73,740 |
| 9 |
605,302 |
884 |
69,531 |
| 10 |
628,109 |
968 |
68,543 |
| 11 |
594,105 |
1,102 |
64,693 |
| 12 |
658,305 |
1,117 |
70,418 |
| 13 |
467,872 |
977 |
50,653 |
| 14 |
496,824 |
852 |
54,644 |
| 15 |
563,600 |
736 |
60,307 |
| 16 |
479,831 |
785 |
52,312 |
| 17 |
454,188 |
722 |
51,040 |
| 18 |
378,391 |
604 |
40,948 |
| 19 |
370,300 |
787 |
39,877 |
| 20 |
449,443 |
744 |
49,207 |
| 21 |
410,810 |
612 |
44,478 |
| 22 |
335,787 |
520 |
36,763 |
| 23 |
420,876 |
676 |
42,587 |
| 24 |
371,270 |
632 |
40,919 |
| 25 |
269,464 |
430 |
27,099 |
| 26 |
316,133 |
507 |
34,077 |
| 27 |
287,872 |
470 |
32,574 |
| 28 |
290,731 |
482 |
31,154 |
| 29 |
350,281 |
665 |
36,219 |
| X (non PAR) |
285,956 |
486 |
44,949 |
| X (PAR) | 79,554 | 119 | 8,253 |
Multi-sample variant calling was performed as described in Methods. The X chromosome was divided into a pseudoautosomal region (PAR) and a non-pseudoautsomal region (PAR) (see Additional file 9).