Table 1 Archaic SNPs in the LWK population (1000 genome project). The table indicates the average number of block SNPs and singletons in the archaic linkage blocks of LWK and summarizes the distribution of the archaic alleles in structurally defined genomic sub-regions as well as in regions defined by ChIP-seq tracks. Numbers indicate the absolute count of archaic SNPs detected in the region; numbers in brackets indicate the percentage in reference to the total amount of the respective SNP type
Type of archaic SNP | Average number of SNPs per linkage block* | Distribution of archaic SNPs | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
Complete genome | Genic region | HLA genes (MHC I and II) | CpG Island (CGI) | Open chromatin (DNase I)a | Recomb. hotspot (DCM1)b | H3K4me3/H3K27me3 (bivalent)a | 5mC tracksc | 5hmC tracksd | ||
Block SNP | 4.30 | 1021071 | 379447 | 5278 | 9105 | 178314 | 10424 | 33888 | 776586 | 11914 |
(53.81) | (37.16) | (0.52) | (0.89) | (17.46) | (1.02) | (3.32) | (88.60) | (1.17) | ||
Singleton | 3.69 | 876329 | 353376 | 3025 | 15175 | 196934 | 56698 | 49900 | 656974 | 22400 |
(46.19) | (40.32) | (0.35) | (1.73) | (22.47) | (6.47) | (5.69) | (86.90) | (2.56) | ||
Total | 8.00 | 1897400 | 732823 | 8303 | 24280 | 375248 | 67122 | 83788 | 1433560 | 34314 |
(100.00) | (38.62) | (0.44) | (1.28) | (19.78) | (3.54) | (4.42) | (87.81) | (1.81) | ||