Table 1A.
SNPs found by NGS in J Haplogroup Cybrids.
| Loci: MT- | SNP | AA Change | Locus | rs# | CY 10-01 | CY 10-05 | CY 11-32 | CY 12-43 | CY 13-62 | CY 13-74 | CY 13-107 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| CR:HV2/OHR | 152 T>C | NonCoding | rs117135796 | J1d | |||||||
| CR:HV2/OHR | 185 G>A | NonCoding | na | J1c | J1c | ||||||
| CR:HV2/OHR | 200 A>G | NonCoding | rs372099630 | 8.28% Htroplsmy |
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| CR:HV2/OHR | 228 G>A | NonCoding | rs41323649 | J1c | J1c | J1c | |||||
| CR:HV2/OHR | 242 C>T | NonCoding | na | J1b1a | |||||||
| CR:HV2/OHR | 271 C>T | NonCoding | na | J1b1b | |||||||
| CR:HV2/OHR | 295 C>T | NonCoding | rs41528348 | J | J | J | J | J | J | J | |
| CR:HV3 | 462 C>T | NonCoding | rs41402146 | J1 | J1 | J1 | J1 | J1 | J1 | J1 | |
| CR:HV3 | 482 T>C | NonCoding | rs386419941 | J1c1 | J1c1 | ||||||
| CR:HV3 | 489 T>C | NonCoding | rs28625645 | J | J | J | J | J | J | J | |
| tRNA Phe | 596 T>C | tRNA | na | 5.4% Htroplsmy |
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| RNR1 | 1007 G>A | rRNA | rs111033213 | J1d1a | |||||||
| RNR2 | 2158 T>C | rRNA | rs41349444 | J1b1a | |||||||
| RNR2 | 2305 T>C | Unique | na | PVT-b | |||||||
| RNR2:Hum | 2655 G>A | Unique | na | 7.95% Htroplsmy |
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| RNR2 | 3010 G>A | rRNA | rs3928306 | J1 | J1 | J1 | J1 | J1 | J1 | J1 | |
| RNR2 | 3197 T>C | rRNA | rs2854131 | 6.79% Htroplsmy |
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| TER/TL1 | 3242 G>A | tRNA | rs193303018 | 17.29% Htroplsmy |
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| ND1 | 3394 T>C | Tyr30His | rs41460449 | J1c1 | J1c1 | ||||||
| ND1 | 3847 T>C | Syn:Leu181 | na | PVT-a | |||||||
| ND1 | 4216 T>C | Tyr304His | rs1599988 | JT | JT | JT | JT | JT | JT | JT | |
| ND2 | 5460 G>A | Ala331Thr | rs3021088 | J1b1 | J1b1 | ||||||
| tRNA Cys | 5821 G>A | tRNA | rs200587831 | 3.44% Htroplsmy |
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| CO1 | 6261 G>A | Ala120Thr | rs201262114 | PVT-a | |||||||
| CO1 | 6554 C>T | Syn:Thr217 | na | J1c7 | |||||||
| CO1 | 6734 G>A | Syn:Met277 | rs41413745 | PVT-b | |||||||
| CO1 | 6899 G>A | Syn:Met332 | na | PVT-b | |||||||
| CO1 | 7146 A>G | Thr415Ala | rs372136420 | 3.25% Htroplsmy |
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| CO1 | 7226 G>A | Syn:Ser441 | rs369835151 | PVT-b | |||||||
| CO1 | 7256 C>T | Syn:Asn451 | rs41542322 | 4.2% Htroplsmy |
3.1% Htroplsmy |
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| CO2 | 7747 C>T | Syn:Asn54 | rs28608702 | J1b1b1c | |||||||
| CO2 | 7789 G>A | Syn:Leu68 | rs386829014 | J1d | |||||||
| CO2 | 7805 G>A | Val74Ile | na | PVT-b | |||||||
| CO2 | 7963 A>G | Syn:Leu126 | na | J1d | |||||||
| CO2 | 8192 A>G | Asn203Tyr | na | 3.24% Htroplsmy |
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| CO2 | 8200 T>C | Syn:Ser205 | na | PVT-b | |||||||
| CO2 | 8269 G>A | Syn:Ter228 | na | J1b | J1b | J1b | |||||
| ATP8/ATP6 | 8557 G>A | Syn:Leu64/Ala11Thr | rs386829040 | J1b1a | |||||||
| CO3 | 9635 A>C | Syn:Ser143 | na | J1c1a | |||||||
| ND3 | 10398 A>C | Thr114Ala | rs2853826 | J | J | J | J | J | J | J | |
| tRNA Arg | 10410 T>A | tRNA | rs200478835 | J1b1b1 | |||||||
| ND4L | 10654 C>T | Ala62Val | na | PVT-b | |||||||
| ND4 | 11251 A>G | Syn:Leu164 | rs3915952 | JT | JT | JT | JT | JT | JT | JT | |
| ND4 | 11623 C>T | Syn:Tyr288 | na | J1c1a | |||||||
| ND4 | 11827 T>C | Syn:Ala356 | rs368026942 | 10.16% Htroplsmy |
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| ND4 | 12007 G>A | Syn:Trp416 | rs2853497 | J1b1a | |||||||
| ND4 | 12127 G>A | Syn:Gly456 | na | J1c7 | |||||||
| ND5 | 12612 A>G | Syn:Val92 | rs28359172 | J | J | J | J | J | J | J | |
| ND5 | 13143 T>C | Syn:Asn269 | rs386829174 | PVT-b | |||||||
| ND5 | 13708 G>A | Ala458Thr | rs28359178 | J | J | J | J | J | J | J | |
| ND5 | 13879 T>C | Ser515Pro | rs200380057 | J1b1 | J1b1 | ||||||
| ND5 | 13899 T>C | Syn:Tyr521 | rs370031192 | J1c1a | |||||||
| ND6 | 14028 A>G | Syn:Lys564 | na | PVT-b | |||||||
| CYB | 14798 T>C | Phe18Leu | rs28357681 | J1c | J1c | J1c | |||||
| CYB | 15452 C>A | Leu236Ile | rs527236209 | JT | JT | JT | JT | JT | JT | JT | |
| CYB | 15769 A>G | Syn:Gln341 | na | 4.9% Htroplsmy |
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| CR:HV1 | 16069 C>T | NonCoding | rs147903261 | J | J | J | J | J | J | J | |
| CR:TAS2 | 16092 T>C | NonCoding | na | J1c7 | |||||||
| CR:TAS2 | 16126 T>C | NonCoding | rs147029798 | JT | JT | JT | JT | JT | JT | JT | |
| CR:7SDNA | 16145 G>A | NonCoding | rs41419246 | J1b | J1b | J1b | |||||
| CR:HV1 | 16193 C>T | NonCoding | na | J1d | |||||||
| CR:HV1 | 16209 T>C | NonCoding | rs386829278 | PVT-b | |||||||
| CR:HV1 | 16222 C>T | NonCoding | rs386829282 | J1b | |||||||
| CR:HV1 | 16261 C>T | NonCoding | rs138126107 | J1b | J1b | J1b | |||||
| CR:HV1 | 16263 T>A | NonCoding | rs386829294 | J1c7 | PVT-a | ||||||
| CR:HV1 | 16292 C>T | NonCoding | rs144417390 | PVT-a | |||||||
| CR:HV1 | 16300 A>G | NonCoding | na | J1d1 | |||||||
| CR:HV1 | 16309 A>G | NonCoding | rs373517769 | J1d1a |
PVT-a, found in other J or H haplogroups.
PVT-b, not found in other J or H haplogroups.
na:, not available.
All SNP's had a Quality (A Phred-scaled quality score assigned by the variant caller) Score of 100 and PASSed all the Filters.