Table 1.
Genetic markers analysed in the OpenArray, the Y haplogroup they define, the alleles and their call rates (successful genotype calls)
| List of genetic markers analysed | List of genetic markers analysed (continuation) | List of genetic markers analysed (continuation) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Marker | Haplogroupa | Allelesb | Call rate (%) | Marker | Haplogroupa | Allelesb | Call rate (%) | Marker | Haplogroupa | Allelesb | Call rate (%) |
| M216 | C | C/T | 95.8 | P259 | I1d | T/G | 96.6 | M231 | N | G/A | 94.7 |
| M168 | CT | C/T | 98.1 | P215 | I2 | A/G | 95.1 | M128 | N1a | 2-bp del | 97.0 |
| M174 | D | T/C | 97.7 | P37.2 | I2a | T/C | 96.6 | P43 | N1b | G/A | 96.6 |
| M145c | DE | G/A | 96.6 | P41.2 | I2a1 | T/C | 97.3 | P105 | N1c | G/A | 96.2 |
| M203c | DE | G/C | 96.6 | M26 | I2a2 | G/A | 95.5 | M214 | NO | G/C | 96.6 |
| M96 | E | G/C | 98.1 | M223 | I2b | C/T | 96.2 | M119 | O1a | A/C | 99.2 |
| P147 | E1 | T/A | 97.7 | M284 | I2b1 | ACAA/del | 96.2 | P31 | O2 | T/C | 95.8 |
| M33 | E1a | A/C | 95.5 | M379 | I2b2 | GT/del | 97.0 | M122 | O3 | T/C | 98.9 |
| P177 | E1b | C/T | 93.6 | P95 | I2b4 | G/T | 95.1 | M45 | P | G/A | 96.2 |
| P2 | E1b1 | C/T | 97.3 | P123 | IJ | T/C | 94.3 | M242 | Q | C/T | 97.3 |
| M2 | E1b1a | A/G | 97.0 | M304 | J | A/C | 94.3 | M207 | R | A/G | 95.5 |
| M215 | E1b1b | A/G | 97.3 | M267 | J1 | T/G | 95.5 | M173 | R1 | A/C | 93.2 |
| M35 | E1b1b1 | G/C | 95.8 | M62 | J1a | T/C | 95.5 | SRY10831.2 | R1a | G/A | 99.6 |
| M78 | E1b1b1a | C/T | 98.1 | M365 | J1b | A/G | Failed | M56 | R1a1a | A/T | 97.7 |
| V12 | E1b1b1a1 | A/G | 97.3 | M390 | J1c | A/ins | Failed | M157 | R1a1b | A/C | 98.1 |
| V13 | E1b1b1a2 | G/A | 97.0 | P56 | J1d | A/G | 96.6 | M204 | R1a1c | T/G | 95.8 |
| V22 | E1b1b1a3 | T/C | 97.7 | P58 | J1e | T/C | 95.5 | P98 | R1a1d | C/T | Failed |
| V65 | E1b1b1a4 | G/T | 96.2 | M172 | J2 | T/G | 96.6 | PK5 | R1a1e | C/T | 95.8 |
| M81 | E1b1b1b | C/T | 89.8 | M410 | J2a | A/G | 95.5 | M343 | R1b | C/A | 97.3 |
| M123 | E1b1b1c | G/A | 97.7 | M47 | J2a1 | G/A | 96.6 | M18 | R1b1a | 2-bp ins | 96.6 |
| M281 | E1b1b1d | G/A | 97.0 | M340 | J2a10 | G/C | 94.7 | P297 | R1b1b | G/C | 95.8 |
| V6 | E1b1b1e | G/C | 99.6 | M419 | J2a11 | AAAAG/del | 95.8 | M73 | R1b1b1 | 2-bp del | 96.2 |
| P72 | E1b1b1f | G/A | 98.1 | P81 | J2a12 | C/T | Failed | M269 | R1b1b2 | C/T | 96.2 |
| M329 | E1b1c | G/C | 98.1 | P279 | J2a13 | G/A | 98.1 | L23 | R1b1b2a | A/Ge | 84.8 |
| P75 | E1b2 | G/A | Failed | M67 | J2a2 | A/T | 95.1 | P311 | R1b1b2a1 | A/G | 97.0 |
| M75 | E2 | G/A | 97.7 | M92 | J2a2a | T/C | 96.2 | U106 | R1b1b2a1a | C/T | 97.3 |
| M89 | F | C/T | 97.7 | M68 | J2a3 | A/G | 91.3 | U198 | R1b1b2a1a1 | G/A | 98.5 |
| M201 | G | G/T | 95.5 | M137 | J2a4 | T/C | 97.7 | P107 | R1b1b2a1a2 | G/A | Failed |
| M285 | G1 | G/C | 96.6 | M158 | J2a5 | G/A | 97.7 | P312 | R1b1b2a1b | A/Ce | 97.3 |
| P20 | G1a | C/del | 95.8 | M289 | J2a6 | G/A | 96.6 | M65 | R1b1b2a1b1 | A/T | 96.6 |
| P76 | G1b | G/C | 98.9 | M318 | J2a7 | T/C | 97.3 | M153 | R1b1b2a1b2 | T/A | 97.7 |
| P287 | G2 | G/T | 96.6 | M319 | J2a8 | T/A | 97.7 | SRY2627 | R1b1b2a1b3 | C/T | 97.3 |
| P15 | G2a | C/T | 97.7 | M339 | J2a9 | T/G | 97.7 | U152 | R1b1b2a1b4 | C/T | 97.0 |
| M287 | G2b | A/T | 97.0 | M12 | J2b | G/T | 97.0 | M126 | R1b1b2a1b4a | 4-bp del | 97.3 |
| M377 | G2c | A/G | 94.7 | M205 | J2b1 | T/A | 98.1 | M160 | R1b1b2a1b4b | A/C | 96.2 |
| M69 | H | T/C | 97.0 | M241 | J2b2 | G/A | Failed | L21 | R1b1b2a1b5 | C/G | 97.7 |
| M52 | H1 | A/C | 95.5 | M9ad | K | C/G | 97.3 | M37 | R1b1b2a1b5a | C/T | 87.9 |
| Apt | H2 | G/A | 92.8 | M9bd | K | C/G | 97.3 | M222 | R1b1b2a1b5b | G/A | 97.7 |
| M170 | I | A/C | 97.0 | M20 | L | A/G | 94.3 | P66 | R1b1b2a1b5c | G/A | 98.1 |
| M253 | I1 | C/T | 97.0 | M27 | L1 | C/G | 94.7 | M335 | R1b1c | T/A | 96.2 |
| M21 | I1a | A/T | 96.2 | M317 | L2 | GA/del | 94.3 | M124 | R2 | C/T | 98.1 |
| M72 | I1b1 | A/G | 98.1 | M357 | L3 | C/A | 97.3 | M70 | T | A/C | 97.0 |
| P109 | I1c | G/A | 95.8 | P256 | M | G/A | 97.7 | ||||
aHaplogroups are based upon data published by Karafet et al. [8] and on the Internal Society of Genetic Genealogy (ISOGG) 2009 Y-DNA SNP Index website (http://isogg.org/tree/ISOGG_YDNA_SNP_Index09.html).
bThe two alleles of each marker (ancestral or derived) are shown.
cBoth markers (M145 and M203) define the same branch of the human Y-chromosome phylogeny (haplogroup DE).
dMarker M9 was genotyped with two independent assays, with TaqMan probes labelled with different fluorophores (see "SNP selection" inside the Material and Methods section).
eAncestral allele not available.