Table 4.
Metrics in “3mask” and “3mask + 28”, at callset and individual level, before and after VQSR
| Metrics | 3mask | 3mask + 28 | |
|---|---|---|---|
| Counts for the entire callset | |||
| Before VQSR | Biallelic SNPs | 20,312,127 | 20,434,008 |
| Multiallelic SNPs | 85,725 | 94,044 | |
| Total SNPs | 20,397,852 | 20,528,052 | |
| Simple indels | 2,601,657 | 2,564,122 | |
| Complex indels | 737,834 | 816,453 | |
| Total indels | 3,339,491 | 3,380,575 | |
| Singletons | 7,980,292 | 8,123,791 | |
| Biallelic SNPs in dbSNP (%) | 96.67% | 96.67% | |
| Simple indels in dbSNP (%) | 94.29% | 94.21% | |
| After VQSR | Biallelic SNPs | 19,591,088 | 19,544,864 |
| Multiallelic SNPs | 75,115 | 79,945 | |
| Total SNPs | 19,666,203 | 19,624,809 | |
| Singletons (SNPs) | 6,923,568 | 6,902,425 | |
| Filtered SNPs | 731,649 | 903,243 | |
| Biallelic SNPs in dbSNP (%) | 96.88% | 96.96% | |
| Average (and standard deviation (stdev)) per individual | |||
| Before VQSR | Biallelic SNPs (average) | 4,445,566.93 | 4,448,252.21 |
| Biallelic SNPs (stdev) | 438,990.07 | 440,005.98 | |
| Biallelic SNPs (min) | 3,443,131.00 | 3,442,837.00 | |
| Biallelic SNPs (max) | 4,917,928.00 | 4,922,667.00 | |
| Multiallelic SNPs (average) | 32,414.75 | 33,932.54 | |
| Multiallelic SNPs (stdev) | 3961.22 | 4451.22 | |
| Total SNPs (average) | 4,477,981.68 | 4,482,184.75 | |
| Simple indels (average) | 508,597.68 | 490,154.68 | |
| Simple indels (stdev) | 46,465.10 | 46,446.32 | |
| Complex indels (average) | 347,547.21 | 370,585.18 | |
| Complex indels (stdev) | 25,401.04 | 30,851.51 | |
| Total indels (average) | 856,144.89 | 860,739.86 | |
| Singletons (average) | 285,010.43 | 290,135.39 | |
| Singletons (stdev) | 69,862.20 | 70,494.15 | |
| After VQSR | Biallelic SNPs (average) | 4,299,853.14 | 4,305,202.11 |
| Biallelic SNPs (stdev) | 428,861.99 | 430,653.45 | |
| Biallelic SNPs (min) | 3,393,934.00 | 3,394,319.00 | |
| Biallelic SNPs (max) | 4,741,343.00 | 4,749,854.00 | |
| Multiallelic SNPs (average) | 28,645.43 | 29,668.04 | |
| Multiallelic SNPs (stdev) | 3019.16 | 3267.90 | |
| Total SNPs (average) | 4,328,498.57 | 4,334,870.14 | |
| Singletons (SNPs, average) | 247,270.29 | 246,515.18 | |
| Singletons (SNPs, stdev) | 61,967.99 | 62,371.91 | |
| Filtered SNPs (average) | 149,483.11 | 147,314.61 | |
| Filtered SNPs (stdev) | 48,246.66 | 48,020.13 | |
Only SNPs are considered after VQSR. Metrics names in italics have been calculated by the authors (i.e. not an output of Picard’s CollectVariantCallingMetrics)