Comparison of SNP Annotations Between Failed and Functional Assays and Between Polymorphic Classes
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Functionalc |
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|---|---|---|---|---|---|---|---|
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Na |
Failed (N = 21,899) |
Non-Polymorphic (N = 77,809) |
MAFd≤0.05 (N = 12,169) |
MAF >0.05 (N = 114,222) |
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| Heterozygosity | 26,248 | 0.19/0.39/0.49 | 0.01/0.13/0.42 | 0.10/0.24/0.43 | 0.32/0.44/0.49 | ||
| Length | 193,940 | 394/419/551b | 356/401/534 | 401/436/561 | 401/447/548 | ||
| RS Build | 193,940 | 87/92/108b | 86/92/106 | 87/92/108 | 88/100/111 | ||
| NCBI validation | 193,941 | ||||||
| No | 73% (11,077)b | 86% (55,541) | 72% (7,641) | 57% (59,340) | |||
| Yes | 27% (4,157) | 14% (8,683) | 28% (2,929) | 43% (44,573) | |||
| MolType | 193,940 | ||||||
| cDNA | 13% (1,924)b | 18% (11,754) | 9% (948) | 5% (5,397) | |||
| Genomic | 87% (13,310) | 82% (52,470) | 91% (9622) | 95% (98,515) | |||
| SNP Type | 193,932 | ||||||
| Not annotated | 34% (5,219)b | 30% (19,462) | 32% (3,385) | 31% (32,131) | |||
| Intron | 30% (4,608) | 31% (19,962) | 34% (3,614) | 38% (39,046) | |||
| Locus region | 15% (2,227) | 14% (9,301) | 15% (1,571) | 15% (15,491) | |||
| mRNA UTR | 13% (2,002) | 15% (9,720) | 13% (1,331) | 11% (11,718) | |||
| Coding | 0% (30) | 0% (130) | 0% (15) | 0% (94) | |||
| Coding nonsynon | 4% (609) | 5% (3,344) | 3% (358) | 3% (2,663) | |||
| Coding synon | 3% (425) | 3% (1,792) | 2% (243) | 2% (2,287) | |||
| Exception | 1% (110) | 1% (496) | 1% (53) | 0% (465) | |||
| Splice site | 0% (4) | 0% (13) | 0% (0) | 0% (13) | |||
| Submitter count | 193,941 | ||||||
| 1 | 48% (7,382) | 62% (39,822) | 49% (5,203) | 38% (39,873) | |||
| 2 | 33% (5,056) | 28% (17,869) | 35% (3,694) | 38% (39,572) | |||
| 3 | 14% (2,148) | 9% (5,527) | 12% (1,321) | 18% (18,321) | |||
| >3 | 4% (648) | 1% (1,006) | 4% (352) | 6% (6,147) | |||
| RS Mapping | 193,941 | ||||||
| 0 | 8% (1,178)b | 6% (3,885) | 5% (544) | 2% (2,315) | |||
| 1 | 90% (13,746) | 92% (59,280) | 93% (9,819) | 95% (99,185) | |||
| >1 | 2% (310) | 2% (1,059) | 2% (207) | 2% (2,413) | |||
| eXTEND mapping | 226,059 | ||||||
| 0 | 29% (6,281)b | 9% (7,006) | 7% (860) | 7% (7,455) | |||
| 1 | 57% (12,532) | 73% (56,566) | 72% (8,782) | 81% (92,947) | |||
| >1 | 14% (3,085) | 18% (14,208) | 21% (2,526) | 12% (13,811) | |||
| TSC MAF range | 7,997 | ||||||
| [0, 0.025] | 23% (120) | 74% (1,325) | 29% (129) | 5% (239) | |||
| [0.025, 0.05] | 6% (31) | 7% (133) | 22% (99) | 3% (163) | |||
| [0.05, 0.075] | 3% (16) | 3% (59) | 10% (43) | 3% (141) | |||
| [0.075, 0.1] | 5% (28) | 2% (33) | 10% (46) | 5% (282) | |||
| >0.1
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63% (331)
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13% (234)
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29% (130)
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84% (4,415)
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The first eight annotation categories were drawn from NCBI dbSNP for the 193,940 SNPs that overlap with SNPs in this study.
Quantitative variables are summarized as 1st quartile/median/3rd quartile. Categorical variables are summarized by column percent (count).
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↵a N: Number of valid nonmissing observations for each variable.
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↵b Comparisons between failed and functional assays significant at α = 0.05. All significant results have P-values < 10-6.
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↵c All comparisons among functional assay groups are statistically significant with P-values < 10-6.
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↵d MAF: Minor allele frequency.
