Table 2. Clusters of SNPs identified in present study.
| Cluster | LTR | SNPs involved | Total number of SNPs involved | Haplogroup | Position | Length of the cluster (bp) | Donor | Gene conversion tract lengths |
Notes | |
|---|---|---|---|---|---|---|---|---|---|---|
| MIN | MAX | |||||||||
| 1 | LTR-2 | from V351 to V356 | 6 | E-V257* | chrY:2866271–2866356 | 86 | chrY:3966976–3968339 | 86 | 246 | V355 shared SNP with donor (rs371261324) |
| 2 | LTR-2 | V354, V356 | 2 | E-V12* | chrY:2866347–2866356 | 10 | chrY:3966976–3968339 chrX:8419802–8421096 chr7:145393687–145395025 | 10 | 57 | |
| 3 | LTR-2 | V363, V365.2, V366 | 3 | Homoplasic | chrY:2866480–2866496 | 17 | chrY:8166477–8168142 | 3 | 14 | V363 could be generated by mutation or by a GC event (min 1, max 14) |
| 4 | LTR-2 | V364, V365.1, V367 | 3 | B1 | chrY:2866490–2866505 | 16 | chr10:19239555–19240773 | 16 | 69 | |
| 5 | LTR-2 | V372, V374, V375.2, V376 | 4 | A3-M28 | chrY:2866617–2866630 | 14 | chrY:7489271–7490822 chrY:28328893–28330444 chrY:24854475–24856026 chrY:25632458–25634009 | 14 | 41 | Same donors as cluster 8 |
| 6 | LTR-2 | V387, V388 | 2 | A1-M31 | chry:2866786–2866791 | 6 | several putative donors | N.A. | N.A. | |
| 7 | LTR-2 | from V380 to V384 | 5 | B2-P6 | chrY:2866724–2866733 | 10 | chrY:6533820–6535364 | 10 | 89 | |
| 8 | LTR-2 | V389, V390 | 2 | E-M33 | chrY:2866871–2866880 | 10 | chrY:7489271–7490822 chrY:28328893–28330444 chrY:24854475–24856026 chrY:25632458–25634009 | 10 | 74 | Same donors as cluster 5 |
| 9 | LTR-2 | V376, V377 | 2 | E-V22* | chrY:2866630–2866640 | 11 | chr6:8665762–8667845 | 11 | 54 | |
| 10 | LTR-2 | from V390 to V394 | 5 | C-M217 | chrY:2866880–2866931 | 52 | chrY:3966976–3968339 | 24 | 450 | V394 could be generated by mutation or by a GC event from other donors |
| 11 | LTR-2 | from V391 to V393 | 3 | O-M117 | chrY:2866881–2866903 | 23 | chrY:3966976–3968339 chrX:89776222–89776267 | 23 | 34 | |
| 12 | LTR-2 | V370, V371 | 2 | Homoplasic | chrY:2866613–2866613 | 2 | N.A.a | N.A.a | N.A.a | |
| 13 | LTR-2 | V357, V358, V360, V361, V362 | 5 | J-M67* | chrY:2866398–2866421 | 24 | chrY:8166477–8168142 | 24 | 83 | |
| 14 | LTR-24 | from V448 to V455 | 9 | I-M170* | chrY:16709731–16709794 | 63 | chrY:16708816–16710643 | 63 | 96 | INTRA-LTR GC |
| 15 | LTR-24 | V458, V459 | 2 | A3-M51 | chrY:16710137–16710139 | 3 | chrY:16700564–16702229 | 3 | 26 | single-donor GC between HERV-flanking LTRs |
| 16 | LTR-24 | V465, V466 | 2 | B2-M182 | chrY:16710593–16710595 | 3 | chrY:16700564–16702229 | 3 | 49 | single-donor GC between HERV-flanking LTRs |
aNot Analysed. Only clusters >2 bp were analysed.