Skip to main content

Table 1 Summary of total SNPs detected using bcftools for each approach scenario used for comparisons

From: Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle

Approach scenario description

n

Total SNPs before filtering

Total SNPs after filtering

Percentage of SNPs passing all filters (%)

Approach i) non-merged samples

 Liver tissue

6

626,460

258,120

41.20

 Muscle tissue

6

940,143

396,705

42.20

 Liver and Muscle tissue

12

1,205,664

511,092

42.39

Approach ii) merged samples by RFI group

 Liver tissue

6

521,588

197,309

37.82

 Muscle tissue

6

770,685

296,169

38.43

 Liver and Muscle tissue

12

1,005,696

388,322

38.61

Approach iii) merged samples by RFI and tissue group

 Liver and Muscle tissue

12

1,048,370

416,216

39.70

  1. i) non-merged samples; ii) merged samples by group for low-RFI and merged samples for high-RFI for each tissue, iii) merged samples by group and tissue for low- and high-RFI for both tissues
  2. n = total number of samples