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SNPs called on the UMD3.1 assembly using different pipelines.
| 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 |
NQS, Neighbourhood Quality Standard; * pipelines that were implemented with mapping quality.
