Table 3 X and Y chromosome coverage of common resources indexing non-specific probes, and polymorphic probes
Annotation | Citation | Definition of non-specificity | X | Y |
|---|---|---|---|---|
450K array non-specific probe annotations | ||||
Zhou et al. 2017 | [36] | High-quality sequence match to intended target (based on internal score), with unique 30 nucleotide 3ʹ subsequence (MASK.mapping & MASK.sub30.copy) | 1267 | 174 |
Price et al. 2013 | [37] | > 40 nucleotide match with > 90% identity and no gaps, must match at position 50 | 1202 | 146 |
Chen et al. 2013 | [38] | ≥ 47 nucleotide match with no gaps and a match at position 50, only best match retained | 819 | 116 |
EPIC array non-specific probe annotations | ||||
Zhou et al. 2017 | [36] | High-quality sequence match to intended target (based on internal score), with unique 30 nucleotide 3ʹ subsequence (MASK.mapping & MASK.sub30.copy) | 2018 | 217 |
Pidsley et al. 2016 | [8] | ≥ 47 nucleotide homology with at least one off-target locus | 962 | 221 |
Annotation | Citation | SNP reference | Definition of polymorphic | X | Y |
|---|---|---|---|---|---|
450K array polymorphic probe annotations | |||||
Zhou et al. 2017 | [36] | dbSNPv147 + 1KGP.phase3 | MAF > 0.01 within last 5 nucleotides of probe including CpG or SBE, or SNPs that cause a color switch for Type I probes. (MASK.extbase, MASK.typeINextBaseSwitch, & MASK. snp5.GMAF1p) | 145 | 2 |
Illumina | [84] | dbSNPv147 | Polymorphism at CpG or SBE (MAF > 0.01) | 181 | 0 |
Illumina | [84] | dbSNPv132 | Polymorphism at CpG or SBE (MAF > 0.01) | 48 | 0 |
Price et al. 2013 | [37] | dbSNPv131 | Polymorphism at CpG (any MAF, heterozygosity > 0.1 greater effect) | 164 | 9 |
Chen et al. 2013 | [38] | 1KGP.phase1 | Polymorphism at CpG (any MAF) | 0 | 0 |
EPIC array polymorphic probe annotations | |||||
Zhou et al. 2017 | [36] | dbSNPv147 + 1KGP.phase3 | MAF > 0.01 within last 5 nucleotides of probe including CpG or SBE, or SNPs that cause a color switch for Type I probes. (MASK.extbase, MASK.typeINextBaseSwitch, & MASK. snp5.GMAF1p) | 253 | 7 |
Illumina | [84] | dbSNPv147 | Polymorphism at CpG or SBE (MAF > 0.01) | 166 | 0 |
Illumina | [84] | dbSNPv132 | Polymorphism at CpG or SBE (MAF > 0.01) | 45 | 0 |