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Table 6 Numbers of LoF variants before filtering and putative deleterious LoF variants after filtering

From: Deep sequencing of Danish Holstein dairy cattle for variant detection and insight into potential loss-of-function variants in protein coding genes

Variant type Before filtering After filtering
Total (novel) Gene count LoFhom LoFhet AH1 Consistent Inconsistent
Stop gain 395 (210) 345 28 367 97 97 0
Splice site 448 (235) 392 72 376 77 76 1
Frameshift indel 1302 (1123) 931 614 688 171 95 76
Total 2145 (1568)   714 1431 345 268 77
  1. LoFhom variants were homozygous in all four sequenced Danish Holstein cows; LoFhet variants for which at least one of the four sequenced cows was heterozygous; AH1 LoF variants for which none of the 288 sequenced Holstein animals from the 1000 bull genomes project was homozygous; Consistent are concordantly called both in the four Danish Holstein cows and the 288 Holstein animals; Inconsistent variants called as discordant variant types (SNP as indel or indel as SNP) between the four Danish Holstein cows and the 288 bulls from the 1000 bull genomes project; Novel variants are not annotated in dbSNP build133
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