Table 2.
USH2A p.C759F associated haplotypes of six individuals.
| Chr1 position |
Distance (bp) | ID | Freq | REF | ALT | NEI_227 | MEP_109 | BLL_124 | FBP_461 | RKK_75 | RKK_87 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 216219781 | +200679 | rs6657250 | 0.6716 | A | G | AA | AA | AA | AA | AA | AB |
| 216221721 | +198739 | rs10864227 | 0.4636 | C | T | AA | AA | AB | BB | AA | AA |
| 216258213 | +162247 | rs56222536 | 0.1420 | A | G | BB | BB | BB | BB | BB | BB |
| 216270618 | +149842 | rs7540411 | 0.1313 | G | A | BB | BB | BB | BB | BB | BB |
| 216348449 | +72011 | rs55761862 | 0.0651 | A | C | BB | BB | BB | BB | BB | BB |
| 216373804 | +46656 | rs523689 | 0.9591 | T | G | BB | BB | BB | BB | BB | BB |
| 216390475 | +29985 | rs419767 | 0.9590 | C | T | BB | BB | BB | BB | BB | BB |
| 216420460 | 0 (C759F) | rs80338902 | 0.0014 | C | A | BB | BB | BB | BB | BB | BB |
| 216420480 | −20 | rs111033281 | 0.0010 | A | G | AA | AB | BB | BB | BB | BB |
| 216592003 | −171543 | rs4253963 | 0.6486 | T | C | BB | BB | BB | BB | BB | BB |
| 216595306 | −174846 | rs10779261 | 0.7063 | C | T | BB | BB | BB | BB | BB | BB |
Original variant calling format (VCF) files of target capture sequencing data were used for identifying the haplotypes of six individuals with homozygous C759F genotype. Distance, the genomic distance from the C759F variant; ID, dbSNP ID; Freq, the frequency of the alternative allele; REF, reference allele; ALT, alternative allele; AA, homozygous reference; AB, heterozygous; BB, homozygous alternative. The results show that all six individuals share a 199kb haplotype between Chr1:216221721 to Chr1: 216420480. The genomic coordinates are based on hg19.