Table 3.
Metrics in “BP2019”, “BP2015”, and “3mask”, at callset and individual level, before and after VQSR
| Metrics | BP2019 | BP2015 | 3mask | |
|---|---|---|---|---|
| Counts for the entire callset | ||||
| Before VQSR | Biallelic SNPs | 20,301,167 | 20,301,911 | 20,312,127 |
| Multiallelic SNPs | 85,510 | 85,517 | 85,725 | |
| Simple indels | 2,599,873 | 2,601,041 | 2,601,657 | |
| Complex indels | 737,325 | 738,010 | 737,834 | |
| Singletons | 7,975,044 | 7,974,844 | 7,980,292 | |
| Biallelic SNPs in dbSNP (%) | 96.68% | 96.68% | 96.67% | |
| Simple indels in dbSNP (%) | 94.30% | 94.30% | 94.29% | |
| After VQSR | Biallelic SNPs | 19,619,238 | 19,596,831 | 19,591,088 |
| Multiallelic SNPs | 75,300 | 75,132 | 75,115 | |
| Singletons (SNPs) | 6,930,326 | 6,921,952 | 6,923,568 | |
| Filtered SNPs | 692,139 | 715,465 | 731,649 | |
| Biallelic SNPs in dbSNP (%) | 96.87% | 96.88% | 96.88% | |
| Average (and standard deviation (stdev)) per individual | ||||
| Before VQSR | Biallelic SNPs (average) | 4,443,858.18 | 4,444,067.04 | 4,445,566.93 |
| Biallelic SNPs (stdev) | 438,889.45 | 438,945.07 | 438,990.07 | |
| Biallelic SNPs (min) | 3,442,414 | 3,442,476 | 3,443,131 | |
| Biallelic SNPs (max) | 4,916,206 | 4,916,439 | 4,917,928 | |
| Multiallelic SNPs (average) | 32,357.82 | 32,354.79 | 32,414.75 | |
| Multiallelic SNPs (stdev) | 3943.62 | 3943.33 | 3961.22 | |
| Simple indels (average) | 508,131.89 | 508,474.93 | 508,597.68 | |
| Simple indels (stdev) | 46,623.55 | 46,488.14 | 46,465.10 | |
| Complex indels (average) | 346,817.75 | 347,534.14 | 347,547.21 | |
| Complex indels (stdev) | 25,452.05 | 25,499.59 | 25,401.04 | |
| Singletons (average) | 284,823.00 | 284,815.86 | 285,010.43 | |
| Singletons (stdev) | 69,889.22 | 69,906.60 | 69,862.20 | |
| After VQSR | Biallelic SNPs (average) | 4,302,149.93 | 4,301,534.07 | 4,299,853.14 |
| Biallelic SNPs (stdev) | 429,408.28 | 428,949.56 | 428,861.99 | |
| Biallelic SNPs (min) | 3,393,736 | 3,394,064 | 3,393,934 | |
| Biallelic SNPs (max) | 4,744,903 | 4,743,518 | 4,741,343 | |
| Multiallelic SNPs (average) | 28,690.14 | 28,664.71 | 28,645.43 | |
| Multiallelic SNPs (stdev) | 3028.99 | 3022.11 | 3019.16 | |
| Singletons (SNPs, average) | 247,511.64 | 247,212.57 | 247,270.29 | |
| Singletons (SNPs, stdev) | 62,155.76 | 61,953.47 | 61,967.99 | |
| Filtered SNPs (average) | 145,375.93 | 146,223.04 | 149,483.11 | |
| Filtered SNPs (stdev) | 46,580.10 | 46,955.26 | 48,246.66 | |
Only SNPs are considered after VQSR