TABLE 1.
Summary of library, trimming, and alignment of reads to A. hypogaea genome in each library.
| Genotype | Sample type | Input read pairs | Both surviving | Forward only surviving | Reverse only surviving | Dropped | Overall alignment rate (%) |
| Tifrunner | Control | 43,170,429 | 37,947,881 (87.90%) | 3,481,624 (8.06%) | 608,537 (1.41%) | 1,132,387 (2.62%) | 77.60 |
| Tifrunner | Control | 48,861,831 | 43,973,662 (90.00%) | 3,082,838 (6.31%) | 754,300 (1.54%) | 1,051,031 (2.15%) | 73.40 |
| Tifrunner | Control | 43,839,412 | 39,489,936 (90.08%) | 2,774,014 (6.33%) | 685,366 (1.56%) | 890,096 (2.03%) | 76.90 |
| 587 | Control | 40,070,955 | 36,200,463 (90.34%) | 2,424,462 (6.05%) | 624,743 (1.56%) | 821,287 (2.05%) | 79.30 |
| 587 | Control | 44,781,655 | 40,323,747 (90.05%) | 2,875,811 (6.42%) | 656,639 (1.47%) | 925,458 (2.07%) | 72.90 |
| 587 | Control | 44,683,142 | 40,559,180 (90.77%) | 2,486,187 (5.56%) | 704,413 (1.58%) | 933,362 (2.09%) | 73.20 |
| 506 | Control | 46,447,905 | 41,940,433 (90.30%) | 2,887,090 (6.22%) | 689,080 (1.48%) | 931,302 (2.01%) | 64.80 |
| 506 | Control | 47,081,614 | 42,489,538 (90.25%) | 2,967,321 (6.30%) | 710,662 (1.51%) | 914,093 (1.94%) | 65.90 |
| 506 | Control | 48,467,014 | 43,354,569 (89.45%) | 3,122,297 (6.44%) | 839,644 (1.73%) | 1,150,504 (2.37%) | 75.50 |
| C76-16 | Control | 44,107,057 | 30,307,111 (68.71%) | 1,502,648 (3.41%) | 9,723,368 (22.04%) | 2,573,930 (5.84%) | 67.90 |
| C76-16 | Control | 44,738,941 | 39,605,524 (88.53%) | 3,111,979 (6.96%) | 757,947 (1.69%) | 1,263,491 (2.82%) | 62.20 |
| C76-16 | Control | 44,941,724 | 40,406,587 (89.91%) | 2,744,593 (6.11%) | 770,588 (1.71%) | 1,019,956 (2.27%) | 67.70 |
| Tifrunner | Treatment | 44,640,385 | 39,841,817 (89.25%) | 2,962,824 (6.64%) | 805,756 (1.80%) | 1,029,988 (2.31%) | 78.70 |
| Tifrunner | Treatment | 34,479,724 | 30,039,097 (87.12%) | 2,622,507 (7.61%) | 691,319 (2.01%) | 1,126,801 (37.00%) | 78.50 |
| Tifrunner | Treatment | 44,888,435 | 39,964,474 (89.03%) | 3,022,199 (6.73%) | 830,020 (1.85%) | 1,071,742 (2.39%) | 77.40 |
| 506 | Treatment | 43,660,502 | 39,093,910 (89.54%) | 2,863,022 (6.56%) | 722,662 (1.66%) | 980,908 (2.25%) | 70.80 |
| 506 | Treatment | 37,280,523 | 32,601,953 (87.45%) | 3,329,725 (8.93%) | 591,735 (1.59%) | 757,110 (2.03%) | 78.60 |
| 506 | Treatment | 50,216,886 | 43,881,482 (87.38%) | 4,466,693 (8.89%) | 803,551 (1.60%) | 1,065,160 (2.12%) | 71.50 |
| 587 | Treatment | 49,500,427 | 43,151,072 (87.17%) | 4,570,321 (9.23%) | 773,842 (1.56%) | 1,005,192 (2.03%) | 74.40 |
| 587 | Treatment | 41,764,992 | 36,311,859 (86.94%) | 3,889,085 (9.31%) | 667,580 (1.60%) | 896,468 (2.15%) | 75 |
| 587 | Treatment | 44,072,172 | 38,394,486 (87.12%) | 4,033,529 (9.15%) | 702,205 (1.59%) | 941,952 (2.14%) | 75.10 |
| C76-16 | Treatment | 47,419,319 | 41,051,649 (86.57%) | 4,630,751 (9.77%) | 720,477 (1.52%) | 1,016,442 (2.14%) | 74.90 |
| C76-16 | Treatment | 40,858,205 | 35,399,986 (86.64%) | 3,911,482 (9.57%) | 635,605 (1.56%) | 911,132 (2.23%) | 72.40 |
| C76-16 | Treatment | 39,895,848 | 34,661,111 (86.88%) | 3,699,491 (9.27%) | 652,797 (1.64%) | 882,449 (2.21%) | 77.40 |