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Table 2 Results of approach comparisons showing total SNP identified unique within approach and shared between both approaches

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 comparisons

 

Approach i) v.s. Approach ii)

 

Liver Non-merged v.s. Liver Merged by RFI group

 

Non-merged

Shared

Merged by RFI

Total

Total number of SNPs

61,158

196,962

347

258,467

Percentage of SNPs

23.66

76.20

0.13

 
 

Approach i) v.s. Approach ii)

 

Muscle Non-merged v.s. Muscle Merged by RFI group

 

Non-merged

Shared

Merged by RFI

Total

Total number of SNPs

101,047

295,658

511

397,216

Percentage of SNPs

25.44

74.43

0.13

 
 

Approach i) v.s. Approach iii)

 

Liver and Muscle Non-merged v.s. Liver and Muscle Merged by RFI group and Tissues

 

Non-merged

Shared

Merged by tissues

Total

Total number of SNPs

120,301

390,791

25,425

536,517

Percentage of SNPs

22.42

72.84

4.74

 
 

Approach ii) v.s. Approach iii)

 

Liver and Muscle Merged by RFI group v.s. Liver and Muscle Merged by RFI group and Tissues

 

Merged by RFI

Shared

Merged by tissues

Total

Total number of SNPs

14,699

373,623

42,593

430,915

Percentage of SNPs

3.41

86.70

9.88

 
  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