|
Pipeline
|
Consistent
|
Homozygous > heterozygous
|
As indel
|
Inconsistent
|
|---|
|
BWA + SAMtools
|
253,102 (99.9%)
|
247 (0.1%)
|
107
|
16
|
|
CLC Genomics Workbench
|
254,195 (99.6%)
|
848 (0.3%)
|
101
|
28
|
|
Mosaik + GigaBayes
|
236,261 (97.8%)
|
3,522 (1.4%)
|
1,860 (0.8%)
|
20
|
|
SMALT + SAMtools
|
247,805 (99.8%)
|
272 (0.1%)
|
96
|
19
|
- Consistent, the same alleles at the same sites were determined by both the chip and resequencing methods; Homozygous > heterozygous, homozygous SNPs called on the chip that were over-called as heterozygous in the resequencing pipelines; As indels, SNP sites on the BovineHD BeadChip that were called as indels in resequencing pipelines; Inconsistent, homozygous calls with both the BovineHD BeadChip and the resequencing pipelines but with different alleles.
