Skip to main content

Table 2 Heterozygous genotype consistencies

From: The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data

  

Stricta

Looseb

Sample A

sample B

Consistency Ac

Consistency Bd

Consistency Ac

Consistency Bd

DNA-NB

DNA-NT

0.99

0.97

0.99

0.98

DNA-NB

DNA-TP

0.98

0.99

0.99

0.99

DNA-NB

RNA-NT

0.90

0.80

0.91

0.83

DNA-NB

RNA-TP

0.84

0.83

0.87

0.85

DNA-NT

DNA-TP

0.96

0.98

0.97

0.99

DNA-NT

RNA-NT

0.89

0.79

0.90

0.82

DNA-NT

RNA-TP

0.82

0.83

0.86

0.85

DNA-TP

RNA-NT

0.90

0.79

0.91

0.82

DNA-TP

RNA-TP

0.84

0.83

0.87

0.85

RNA-NT

RNA-TP

0.82

0.87

0.86

0.91

  1. aStrict means if two genotypes are consistent, their genotype call from Unifiedgenotyper has to agree
  2. bLoose means if two genotypes are consistent, their alternative alleles has to be supported by at least 1 read with BQ > 20 at that position
  3. cThe genotype consistency is computed with the number of heterozygous genotypes of sample A as denominator
  4. dThe genotype consistency is computed with the number of heterozygous genotypes of sample B as denominator