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Table 2 Number of variants identified using the respective genotyping methods, from the bovine genome using DNA chip and from the transcriptome of the macrophages using RNA-seq

From: Genome-wide association analysis identified both RNA-seq and DNA variants associated to paratuberculosis in Canadian Holstein cattle ‘in vitro’ experimentally infected macrophages

Genotyping Method

Total variants a

Significantb variants identified by GWAS

p ≤ 5 × 10− 4

p ≤ 5 × 10−5

p ≤ 5 × 10− 6

p ≤ 5 × 10− 7

p ≤ 5 × 10− 8

DNA chip

46,891

     

RNA-seq

763,723

     

Merge (with indel)

1,356,248

787

143

23

3

2

  1. a Post-filtration considering call rate, MAF = 5e-3, HWE = 1e-4, genotype quality, and read depth
  2. bAll variants were corrected at FDR = 0.05. For low MAF variants a suggestive threshold of 5e-4 was used
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BMC Genomics

ISSN: 1471-2164

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