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Table 3 Variant statistics for both genome builds

From: Alternate-locus aware variant calling in whole genome sequencing

  GRCh37 GRCh38
Chromosome All Common Rare Phred All Common Rare Phred
1 344158 299500 44659 503.42 359530 291704 67825 473.83
2 354113 247585 106528 506.54 361469 243400 118069 492.91
3 295447 268021 27426 503.76 301985 263993 37993 492.99
4 319988 290080 29908 515.41 324134 285405 38729 507.33
5 266077 235462 30615 498.58 272482 231747 40734 485.57
6 280789 252705 28084 495.02 279132 246545 32588 487.11
7 249980 220543 29437 488.95 257917 216669 41248 475.69
8 229332 204823 24509 499.70 229541 200845 28696 490.15
9 192615 162202 30413 475.09 200034 159119 40916 466.46
10 217957 194385 23572 508.74 229352 190658 38694 494.18
11 219134 197412 21722 522.84 228324 194132 34192 498.04
12 205085 184477 20608 502.78 212789 175990 36799 483.94
13 166128 151271 14856 530.31 180521 148870 31651 494.65
14 141971 124790 17181 503.15 140443 122524 17919 495.75
15 130324 112085 18239 505.95 131389 109741 21648 493.46
16 134293 116224 18069 487.40 136799 113589 23210 473.36
17 118096 102300 15796 479.64 130637 99074 31563 452.99
18 124509 111958 12552 516.80 132628 110349 22279 485.89
19 98104 84416 13688 456.51 99625 82875 16750 455.35
20 90490 79709 10781 486.09 112562 78562 33999 475.40
21 69511 55211 14300 525.23 73027 53052 19975 513.27
22 59660 50242 9418 455.99 71112 48961 22151 445.27
Total 4307761     4465432    
  1. The mean counts of autosomal variants and the median Phred scores per chromosome are shown for GRCh37 and GRCh38.
  2. Columns: All: all detected variants; Common: listed in dbSNP common_all_*; Rare: variants that are not common.
  3. The mean variant counts for chromosome X were 127,914 (GRCh37) and 132,177 (GRCh38). For chromosome Y, the mean counts could not be estimated since gender information was not available for all of the 121 in-house genomes. Both genome releases include the identical mitochondrial reference (NC_012920.1) with 27 variants