Table 2 Summary of the quality control

From: Mitochondrial genetic variants identified to be associated with posttraumatic stress disorder

Chip

mtSNPs

mtSNPs excluded

Sample size

ISNP

Itot

Intensity ratio outliers

  

UB

no_B38

    

Affy. 6.0

411

0

54

739

3

1 822 374

194 (<0.05%)

Affy. Axiom

213

39

0

1185

4

2 019 240

33 (<0.05%)

Illum. Exome

226

0

0

1177

1

5 32 004

146 (<0.05%)

Illum. Metabo

126

0

9

1216

1

306 432

73 (<0.05%)

  1. The number of mitochondrial single-nucleotide polymorphisms (mtSNPs) refers to the SNPs that passed quality control. Several mtSNPs were excluded due to the upper bound cutoff (UB)39 or because the basepair position was not available in Build 38 (no_B38). Sample size is based on the particular chip. One person may be present on more than one chip. ISNP stands for the number of intensity measures per allele. Itot represents the total number of intensity measures in the sample (ISNP × 2 × sample size × mtSNPs). Each mtSNP contains two intensities (allele A and allele B) and one intensity ratio (A/B). For example, for the Illumina (Illum.) Metabo we have 1216 individuals resulting in 2432 intensities (1216 ratios) per mtSNP. For all 126 mtSNPs (306 432 intensities and 153 216 ratios), only 73 intensity ratios were detected as outliers corresponding to 0.04%. Only the outlier (intensity ratio for that particular person) is removed and the mtSNP remains in the analysis. Affy., Affymetrix.
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