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Table 1 SNPs called on the UMD3.1 assembly using different pipelines.

From: Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

Tools Algorithm SNPs Homozygous Heterozygous
BWA + SAMtools Bayesian * 4,434,826 2,164,136 2,270,690
CLC Genomics Workbench NQS 4,740,179 1,997,225 2,742,954
SMALT + SAMtools Bayesian * 4,077,556 2,144,671 1,932,885
Mosaik + GigaBayes Bayesian 3,993,407 1,732,242 2,261,165
  1. NQS, Neighbourhood Quality Standard; * pipelines that were implemented with mapping quality.