TABLE 2.
Pairwise concordance of SNP data between both variant callers and bead array.
| Breed | Freebayes and bead array a | GATK-HC and bead array a | Freebayes and GATK-HC |
|---|---|---|---|
| MARC III Composite | 96.01 | 95.53 | 99.27 |
| Polypay | 95.70 | 94.89 | 99.23 |
| East Friesian x Lacaune | 95.73 | 95.54 | 99.52 |
| Targhee | 95.87 | 95.65 | 99.57 |
| Dorset | 96.10 | 95.60 | 99.32 |
| Finn | 95.91 | 95.14 | 98.94 |
| Katahdin | 96.02 | 95.34 | 99.08 |
| Texel | 96.16 | 95.77 | 99.46 |
| Hampshire | 95.89 | 95.39 | 99.56 |
| Suffolk | 96.00 | 95.26 | 99.03 |
| Rambouillet | 96.11 | 95.61 | 99.33 |
| Dorper | 96.13 | 95.73 | 99.41 |
| Romanov | 96.10 | 95.58 | 99.29 |
| St. Croix | 95.92 | 95.77 | 99.49 |
| Average | 95.98 | 95.49 | 99.32 |
a
Concordance was calculated using 40,426 SNPs, from the Illumina and Affymetrix bead arrays called by both variant callers.