Table 2 Summary of variant calls generated using the UnifiedGenotyper from the GATK package
Types of variable sites | Number of sites |
|---|---|
Total number of biallelic sites called | 782,717 |
Small insertions/deletions | 89,417 |
SNPs | 693,300 |
Informative SNPs with adequate read coverage in both isolates | 557,819 |
Informative sites with the same genotype call in both isolates | 210,443 |
Discriminatory sites with different genotype call in each isolate | 347,376 |
Discriminatory sites heterozygous in MCCFC | 71,264 |
Discriminatory sites heterozygous in RKQQC | 104,945 |