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How the number of Actual calls made can be greater than Confidently called bases ?
I am working with de novo assembly and I aligned reads to the scaffolds and called SNPs across the samples. But the result I received after Calling for all confident sites (using Unified Genotyper) is quite unusual to me.
This is what I get:
INFO 22:57:01,315 UnifiedGenotyper - Visited bases 1073801052 INFO 22:57:01,339 UnifiedGenotyper - Callable bases 977317465 INFO 22:57:01,349 UnifiedGenotyper - Confidently called bases 575018059 INFO 22:57:01,357 UnifiedGenotyper - % callable bases of all loci 91.015 INFO 22:57:01,366 UnifiedGenotyper - % confidently called bases of all loci 53.550 INFO 22:57:01,374 UnifiedGenotyper - % confidently called bases of callable loci 58.836 INFO 22:57:01,382 UnifiedGenotyper - Actual calls made 698376287
My question is how the number of Actual calls made is greater than the number of Confidently called bases as I always expect Confidently called bases would be greater or equal to Actual calls made but not less.
I would appreciate your help.