TABLE 1.
Sample # | Raw reads number | Mapped reads number | Mapped reads, % | Mean coverage | Ts/Tv ratio | Raw SNPs number | Raw indels number | Filtered SNPs number | Filtered indels number |
---|---|---|---|---|---|---|---|---|---|
1 | 135419040 | 134973712 | 99.67 | 2.65 | 2.01 | 1170490 | 94591 | 1132716 | 92585 |
2 | 152651625 | 152180976 | 99.69 | 3.00 | 2 | 1338431 | 115651 | 1296133 | 113359 |
3 | 135166473 | 134674889 | 99.64 | 2.64 | 1.98 | 1156025 | 100851 | 1119445 | 98894 |
4 | 138380470 | 137897091 | 99.65 | 2.71 | 2.01 | 1187357 | 97416 | 1149187 | 95394 |
5 | 138247447 | 137870773 | 99.73 | 2.72 | 1.98 | 1197711 | 105756 | 1160354 | 103601 |
6 | 170747873 | 170301203 | 99.74 | 3.36 | 1.98 | 1504990 | 139290 | 1455811 | 136558 |
7 | 156619056 | 156211771 | 99.74 | 3.08 | 1.98 | 1389524 | 126783 | 1345519 | 124277 |
8 | 167468957 | 167046801 | 99.75 | 3.29 | 1.99 | 1468924 | 133239 | 1422379 | 130714 |
9 | 349634959 | 349479692 | 99.96 | 14.13 | 1.98 | 3845412 | 638443 | 3646325 | 619174 |
10 | 354831314 | 354646812 | 99.95 | 14.27 | 1.98 | 3864805 | 644140 | 3662651 | 624830 |
11 | 419085260 | 418962576 | 99.97 | 16.81 | 1.98 | 3381380 | 559592 | 3212089 | 539752 |
12 | 370391660 | 370236765 | 99.96 | 14.93 | 1.99 | 3899130 | 644534 | 3703033 | 624312 |
13 | 305447291 | 305279572 | 99.95 | 12.27 | 1.99 | 3785574 | 617903 | 3587268 | 599639 |
14 | 318191054 | 318037831 | 99.95 | 12.85 | 1.98 | 3789480 | 628848 | 3586741 | 609087 |
15 | 362707535 | 362532795 | 99.95 | 14.62 | 1.98 | 3879120 | 651822 | 3666744 | 631928 |
16 | 384884409 | 384695366 | 99.95 | 15.52 | 1.98 | 3887156 | 660029 | 3676958 | 639700 |
17 | 330816726 | 330647548 | 99.95 | 13.31 | 1.98 | 3809749 | 634330 | 3603943 | 615521 |
18 | 366875825 | 366706680 | 99.95 | 14.78 | 1.98 | 3852608 | 645399 | 3649519 | 625418 |
19 | 366788900 | 366617355 | 99.95 | 14.78 | 1.98 | 3893521 | 654992 | 3691772 | 635218 |
20 | 412081693 | 411940287 | 99.97 | 16.62 | 1.98 | 3933194 | 659427 | 3727201 | 636988 |