Table 6.
SNP counts and crossovers (XO) within alpha block segments 1 to 10 between different haplotype sequence alignments (ID_Hap1 and ID_Hap 2).
| Segment number | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 1 to 10 | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Segment name | OR end | F | V | P | G | H | T | K | A | W | J | F to J | Position and XO SNP | XO within or between (/) RE | |
| Segment size | 2.2 kb | 57 kb | 25 kb | 23 kb | 53 kb | 23.4 kb | 20.4 kb | 19 kb | 15 kb | 51 kb | 34 kb | 320.8 | |||
| Hap sequence comparisons | |||||||||||||||
| ID_Hap 1 | ID_Hap 2 | ||||||||||||||
| 11_A*01:01 | 4_A*03:01 | 12 | 284 | 134 | 198 | 382 | 340 | 330 | 245 | 107 | 180 | 40 | 2,240 | ||
| 2_A*01:01 | 4_A*03:01 | 11 | 280 | 144 | 200 | 388 | 367 | 374 | 248 | 110 | 187 | 38 | 2,336 | ||
| 10_A*02:01 | 4_A*03:01 | 12 | 262 | 32 | 35 | 133 | 328 | 321 | 248 | 343 | 380 | 30 | 2,112 | ||
| 2_A*01:01 | 10_A*02:01 | 9 | 340 | 135 | 194 | 371 | 103 | 55 | 164 | 346 | 380 | 35 | 2,123 | ||
| 5_A*02:01 | 1_A*11:01 | 15 | 280 | 35 | 30 | 517 | 356 | 259 | 80 | 240 | 211 | 27 | 2,035 | ||
| 15_A*26:01 | 78_A*29 | 0 | 4 XO 30 | 137 | 182 | 208 | 69 | 203 | 232 | 148 | 727 | 217 | 2,157 | [F] 56590 G/C | Charlie20a |
| 25_A*30 | 46_A*31 | 13 | 206 | 111 | 152 | 264 | 355 | 260 | 297 | 335 | 491 | 173 | 2,644 | ||
| SNP density | average: SNPs/kb | 4.7 | 4.2 | 4.2 | 6.2 | 6.1 | 11.7 | 12.6 | 11.4 | 15.5 | 7.2 | 2.4 | 7.0 | ||
| 4_A*03:01 | 46_A*31 | 13 | SRR | SRR | SRR | SRR | SRR | SRR | SRR | SRR | SRR | SRR | SRR | ||
| 4_A*03:01 | 49_A*33 | 2 | 279 | 191 | 166 | 236 | 65 | 106 | 268 | 331 | 476 | 169 | 2287 | ||
| 46_A*31 | 49_A*33 | 15 | 245 | 196 | 164 XO 0 | 16 | 7 | 9 | 11 | 11 | 33 | 15 | 707 | [P] 97693 C/T | MICG |
| 4_A*03:01 | 48_A*24/B*15:26N | 11 | 255 | 18 | 27 | 502 | 92/XO/del | del | del | del/XO/175 | 171 | 22 | 1262 | [H] 168684 del | L1/AAAGA/MLT1F1 |
| 4_A*03:01 | 94_A*24 | 10 | 279 | 135 | 194 | 440 | 91/XO/del | del | del | del/XO/175 | 219 | 38 | 1571 | [H] 168684 del | L1/AAAGA/MLT1F1 |
| 5_A*02:01 | 8_A*02:05 | 11 | 268 | 106 | 156 | 371 | 27 XO | 14 | 9 | Assembly errors | 28 | 952 | [H] 168492 G/C | L2/HLA-H/L2 | |
| 10_A*02:01 | 8_A*02:05 | 11 | SRR | SRR | SRR | SRR | SRR XO | 5 | 7 | 13 | XO 199 | 24 | SRR/SPR | [H] 168959 G/C | L2/HLA-H/L2 |
| 10_A*02:01 | 8_A*02:05 | 13 | XO 199 | 24 | SPR/SRR | [W] 224700 C/T | ERV3-16A3 | ||||||||
| 34_A*24 | 48_A*24 | 9 | 73 | 139 | 200 | 229/XO/0 | 1/XO/del | del | del | del/XO/2 | 82 | 39 | 763 | [G] 141380 A/G | HAL1/MICF |
| 34_A*24 | 59_A*24 | 2 | 132 | 141 | 199 | 229/XO/1 | 0/XO/del | del | del | del/XO/2 | 5 | 1 | 710 | [G] 141380 A/G | HAL1/MICF |
| 48_A*24 | 68_A*24 | 9 | 86 | 132 | 199 | 331/XO/1 | 0/XO/del | del | del | del/XO | 89 | 41 | 879 | [G] 144028 G/A | HAL1/MICF |
| 48_A*24 | 94_A*24 | 9 | 88 | 132 | 199 | 334/XO/1 | 0/XO/del | del | del | del/XO | 88 | 42 | 884 | [G] 144028 G/A | HAL1/MICF |
| 59_A*24 | 94_A*24 | 2 | 132 | 136 | 197 | 284/XO/1 | 3/XO/del | del | del | del/XO | 4 | 1 | 760 | [G] 141500 G/A | HAL1/MICF |
| 10_A*02:01 | 13_A*02:01 | 10 | 171+XO | 0 | 0 | 3 | 2 | 1 | 1 | 0 | 0 | 0 | 178 | [F] 53540 G/T | Charlie20a |
| 10_A*02:01 | 67_A*02:04 | 10 | 155+XO | 1 | 1 | 2 | 2 | 0 | 0 | 1 | 0 | 0 | 152 | [F] 53540 G/T | Charlie20a |
| 10_A*02:01 | 76_A*02:04 | 10 | 155+XO | 1 | 1 | 2 | 2 | 0 | 0 | 1 | 0 | 0 | 152 | [F] 53540 G/T | Charlie20a |
| 5_A*02:01 | 13_A*02:01 | 11 | 166+XO | 0 | 0 | 6 | 1 | 3 | 3 | Assembly errors | 3 | 7 | [F] 53275 G/T | Charlie20a | |
| 4_A*03:01 | 18_A*03/A*24 | 5 | 137 | 78 | 126 | 179+XO | 0 | 0 | 2 | 7/XO | 131 | 37 | 692 | [G} 150337 C/T | Tigger1/Charlie20a |
| [A] 229198 G/T | L2/HLA-A/L2 | ||||||||||||||
| 48_A*24 | 59_A*24 | 11 | 139 XO 0 | 1 | 0 | 0 | 0/XO/del | del | del | del/XO | 87 | 42 | 269 | [F} 53185 T/C | Tigger1/Charlie20a |
| 34_A*24 | 68_A*24 | 0 | 0 | 0 | 1 | 1 | XO/del | del | del | del/XO | 1 | 0 | 2 | [H] del [A] | |
| 34_A*24 | 94_A*24 | 0 | 0 | 0 | 1 | 1 | XO/del | del | del | del/XO | 0 | 0 | 1 | [H] del [A] | |
| 10_A*02:01 | 32_A*02:17 | Seq missing | 0 | 1 | 4 | 1 | 0 | 0 | 3 | 0 | 0 | 9 | OR cluster | ||
| 5_A*02:01 | 10_A*02:01 | 1 | 3 | 0 | 0 | 5 | 3 | 2 | 2 | Assembly errors | 3 | 18 | OR cluster | ||
| 11_A*01:01 | 16_A*01:01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 21.5 kb del | 1 | OR cluster | |
| 2_A*01:01 | 16_A*01:01 | 0 | 1 | 1 | 0 | 1 | 3 | 3 | 3 | 32 | 3 | 21.5 kb del | 47 | OR cluster | |
| 2_A*01:01 | 11_A*01:01 | 0 | 1 | 1 | 0 | 1 | 3 | 3 | 3 | 1 | 3 | 2 | 18 | OR cluster | |
| 10_A*02:01 | 17_A*02:17 | 0 | 0 | 0 | 1 | 2 | 1 | 0 | 0 | 3 | 0 | 0 | 7 | OR cluster | |
| 10_A*02:01 | 92_A*02:12 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 2 | 1 | 0 | 6 | OR cluster | |
| 4_A*03:01 | 6_A*03:01 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 3 | OR cluster | |
| 4_A*03:01 | 7_A*03:01 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 1 | 0 | 2 | 1 | 6 | OR cluster | |
| 15_A*26 | 64_A*26 | 0 | 1 | 0 | 1 | 2 | 3 | 0 | 1 | 0 | 4 | 1 | 13 | OR cluster | |
| 15_A*26 | 84_A*26 | 0 | 1 | 0 | 0 | 3 | 1 | 0 | 0 | 0 | 2 | 0 | 7 | OR cluster | |
| 15_A*26 | 69_A*66 | 2 | 10 | 3 | 1 | 15 | 7 | 6 | 1 | 3 | 9 | 8 | 63 | OR cluster | |
| 78_A29 | 79_A29 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | OR cluster | |
| 25_A*30 | 26_A*30 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | OR cluster | |
| 46_A*31 | 73_A*31 | 1 | 1 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 4 | OR cluster | |
| 46_A*31 | 82_A*31 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | OR cluster | |
| 9_A*32 | 22_A*32 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | OR cluster | |
| 9_A*32 | 72_A*32 | 0 | 0 | 1 | 0 | 1 | 1 | 2 | 1 | 0 | 1 | 1 | 8 | OR cluster | |
| 49_A*33 | 50_A*33 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | OR cluster | |
*
The SRR to SPR XO in Seg G (4) at A/G 141380 HAL1 and (ATAAT)n is near the AluHG insertion locus and the MICF pseudogene. XO is the abbreviation for crossover; SRR, SNP-rich region; SPR, SNP-poor region. The numbers before and/or after XO are the number of counted SNPs before and/or after the observed XO. There are XO points outside the alpha block in the telomeric OR gene region and the centromeric non-HLA region between HLA-J and HLA-E. The bold values here show the SNP density and the average number of SNPs/kb for the top 7 haplotype sequence comparisons in the table.