Table 6.
Ti/Tv ratio at each variant-level step in the genome-wide biallelic and triallelic pipelines.
| Filter/Step | Biallelic Sites | Triallelic Sites | ||
|---|---|---|---|---|
| Ti/Tv | Change (%) | Ti/Tv | Change (%) | |
| (1) Original | 1.88322 | — | 1.88322 | — |
| (2) Biallelic (or Triallelic) Only | 2.04350 | +8.511 | 0.94341 | −0.940 |
| (3) ‘PASS’ | 2.14108 | +4.775 | 0.96112 | +0.018 |
| (4) Missingness | 2.14111 | +0.001 | 0.96122 | +0.0001 |
| (5) DP | 2.14874 | +0.356 | 0.94256 | −0.019 |
| (6) MQ | 2.14418 | −0.212 | 0.85855 | −0.084 |
| (7) InbreedingCoeff | 2.14707 | +0.135 | 0.87857 | +0.020 |
| (8) SNV VQSLOD | 2.16381 | +0.780 | 0.85444 | −0.024 |
Ti/Tv increases by 0.12 (5.9%) among biallelic SNVs, from before GATK is run (step 2) through the end of QC. Ti/Tv decreases by 0.089 (9.4%) among triallelic SNV-containing sites (SNV-SNV and SNV-indel).