Table 1.
RADseq results in 18 plants using Hi-seq 2000 NGS platform
| Parents and F1 plants | Read number | Total RAD sequence (bp)* | Number of RAD tags | Total sequence of RAD taqs (bp)** | Coverage depth*** | Sequence coverage**** | GC rate (%) | Total SNP | Heterozygous SNP rate (%) |
|---|---|---|---|---|---|---|---|---|---|
| Females | |||||||||
| Siirt | 15,873,498 | 1,301,626,836 | 422,422 | 34,638,604 | 37.6 | 2.0 | 37.65 | 90,999 | 17.3 |
| P-F-1 | 24,754,856 | 2,029,898,192 | 442,751 | 36,305,582 | 55.9 | 3.1 | 37.12 | 98,348 | 26.9 |
| P-F-2 | 22,527,994 | 1,847,295,508 | 513,815 | 42,132,830 | 43.8 | 2.8 | 37.60 | 97,562 | 28.0 |
| P-F-3 | 28,035,806 | 2,298,936,092 | 513,654 | 42,119,628 | 54.6 | 3.5 | 37.07 | 99,776 | 25.3 |
| P-F-4 | 33,578,112 | 2,753,405,184 | 560,479 | 45,959,278 | 59.9 | 4.2 | 36.86 | 101,339 | 30.5 |
| P-F-5 | 23,563,272 | 1,932,188,304 | 539,390 | 44,229,980 | 43.7 | 2.9 | 37.47 | 98,767 | 31.9 |
| P-F-6 | 23,374,790 | 1,916,732,780 | 523,591 | 42,934,462 | 44.6 | 2.9 | 37.38 | 98,876 | 29.9 |
| P-F-7 | 28,326,906 | 2,322,806,292 | 539,702 | 44,255,564 | 52.5 | 3.5 | 36.88 | 100,355 | 27.4 |
| P-F-8 | 25,474,290 | 2,088,891,780 | 431,895 | 35,415,390 | 59.0 | 3.2 | 37.64 | 96,551 | 17.5 |
| Subtotal | 225,509,524 | 18,491,780,968 | 4,487,699 | 367,991,318 | 451.6 | 28.0 | - | 882,573 | - |
| Subaverage | 25,056,614 | 2,054,642,330 | 498,633 | 40,887,924 | 50.2 | 3.1 | 37.30 | 98,064 | 26.1 |
| Males | |||||||||
| Bağyolu | 27,187,532 | 2,229,377,624 | 552,533 | 45,307,706 | 49.2 | 3.4 | 38.00 | 79,746 | 33.1 |
| P-M-1 | 22,615,328 | 1,854,456,896 | 498,044 | 40,839,608 | 45.4 | 2.8 | 36.98 | 98,046 | 27.2 |
| P-M-2 | 10,108,252 | 828,876,664 | 422,176 | 34,618,432 | 23.9 | 1.3 | 37.10 | 75,521 | 20.5 |
| P-M-3 | 19,417,040 | 1,592,197,280 | 541,272 | 44,384,304 | 35.9 | 2.4 | 37.48 | 95,941 | 26.7 |
| P-M-4 | 11,079,312 | 908,503,584 | 410,036 | 33,622,952 | 27.0 | 1.4 | 38.77 | 72,909 | 18.6 |
| P-M-5 | 38,882,284 | 3,188,347,288 | 657,285 | 53,897,370 | 59.2 | 4.8 | 37.65 | 102,340 | 30.5 |
| P-M-6 | 26,158,302 | 2,144,980,764 | 569,710 | 46,716,220 | 45.9 | 3.2 | 37.58 | 100,049 | 27.0 |
| P-M-7 | 29,947,304 | 2,455,678,928 | 596,268 | 48,893,976 | 50.2 | 3.7 | 37.51 | 99,531 | 27.5 |
| P-M-8 | 39,817,004 | 3,264,994,328 | 623,841 | 51,154,962 | 63.8 | 4.9 | 37.41 | 103,115 | 27.8 |
| Subtotal | 225,212,358 | 18,467,413,356 | 4,871,165 | 399,435,530 | 400.6 | 28.0 | - | 827,198 | - |
| Subaverage | 25,023,595 | 2,051,934,817 | 541,241 | 44,381,726 | 44.5 | 3.1 | 37.61 | 91,911 | 26.5 |
| Total | 450,721,882 | 36,959,194,324 | 9,358,864 | 767,426,848 | 852.2 | 56.0 | 1,709,771 | ||
| Average | 25,040,105 | 2,053,288,574 | 519,937 | 42,634,825 | 47.3 | 3.1 | 37.45 | 94,987 | 26.3 |
*Total RAD sequence was calculated by multiplying read number by 82 bp read length of Illumina.
**Total sequence of RAD taqs was calculated by multiplying number of RAD tags by Illumina 82 bp read length.
***Coverage depth was calculated by dividing Illumina read number by number of RAD taqs.
****Sequence coverage was calculated by dividing total RAD sequence (bp) by the estimated genome size (660 Mbp) of pistachio.