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Table 2 SNP Filter step

From: Sequence imputation from low density single nucleotide polymorphism panel in a black poplar breeding population

Filtering step Freebayes gVCF-GATK
No filter 26,489,941 27,475,756
vcftools (max allele=3, min allele=2, minQ=30) 5,011,303 10,474,367
Monomorphic within P. nigra individuals 1,246,546 2,504,973
Common positions between the two callers 2,488,736 (375,566)
Homology between two callers more than 95% 1,612,432
Consistent Mendelian Segregation 1,466,586 (208,217)
  1. Number of variants detected in the 43 sequenced individuals using two callers with no filter and after filtering with different parameters to obtain the input dataset used for imputation. In brackets, the number of Indels out of the total number of variants