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Table 1 Number of variants detected for each of the 7 calling modalities tested in the present study

From: Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra

Variant calling modality Missing value in genotype calls
  noNA 2NA anyNA
GATK 464,829 555,828 902,256
gVCF_GATK 407,037 497,314 927,522
FreeBayes 492,073 640,445 795,459
Mpileup 496,688 594,932 949,411
3Callers 341,584 366,123 400,392
4Callers 252,887 262,447 271,399
3CallersConsensus 356,275 442,931 785,377
  1. “noNA”: no missing value; “2NA”: lower or equal to 2 missing values; “anyNA”: no filter on missing values. “3Callers”: SNPs detected with at least 3 callers; “4Callers”: SNPs detected with 4 callers; “3CallersConsensus”: SNPs detected with at least 3 callers with correction of the genotype calling when discrepancies existed between callers (see details in Methods)