Table 1.
Summary of RNA sequencing and mapping using the Gossypium hirsutum genome as the reference. Columns represent: number of raw sequencing reads, number of clean reads, percent of reads filtered, GC content, percent of duplicated levels, and ratio of sequences mapped to the genome. HR and ZS correspond to resistant and susceptible cultivars of upland cotton, respectively. The numerical values 1, 2, 3 indicate the different biological replicates, whereas 0, 12, 24, 48 indicate hrs of whitefly infestation. The ZS12 and ZS48 datasets consisted of two replicates, all other datasets correspond to three replicates
| Sample | Total reads | Clean reads | Filter (%) | GC (%) | Dup (%) | Total mapped (%) | Uniquely mapped (%) | Multiple mapped (%) |
|---|---|---|---|---|---|---|---|---|
| HR0‐1 | 45 352 086 | 39 862 040 | 12.11 | 46.00 | 62.79 | 91.20 | 16.46 | 74.74 |
| HR0‐2 | 49 974 678 | 43 839 121 | 12.28 | 46.00 | 68.60 | 93.90 | 16.67 | 77.23 |
| HR0‐3 | 38 733 664 | 35 647 589 | 7.97 | 44.00 | 57.38 | 95.70 | 16.43 | 79.27 |
| HR12‐1 | 51 531 582 | 45 269 773 | 12.15 | 46.00 | 66.66 | 96.00 | 16.83 | 79.17 |
| HR12‐2 | 53 342 506 | 48 236 985 | 9.57 | 46.00 | 71.97 | 90.80 | 14.90 | 75.90 |
| HR12‐3 | 39 824 998 | 35 775 352 | 10.17 | 48.00 | 68.85 | 95.50 | 11.31 | 84.19 |
| HR24‐1 | 48 422 048 | 42 815 229 | 11.58 | 45.00 | 69.54 | 95.60 | 17.36 | 78.24 |
| HR24‐2 | 43 338 340 | 39 663 374 | 8.48 | 44.00 | 61.56 | 93.40 | 16.29 | 77.11 |
| HR24‐3 | 42 433 604 | 38 835 749 | 8.48 | 49.00 | 71.40 | 94.90 | 9.51 | 85.39 |
| HR48‐1 | 43 653 456 | 39 762 828 | 8.91 | 44.00 | 56.76 | 91.60 | 14.99 | 76.61 |
| HR48‐2 | 37 894 414 | 34 315 407 | 9.44 | 44.00 | 55.61 | 92.60 | 15.40 | 77.20 |
| HR48‐3 | 42 486 436 | 38 707 521 | 8.89 | 44.00 | 60.18 | 95.20 | 16.30 | 78.90 |
| ZS0‐1 | 46 625 602 | 41 020 778 | 12.02 | 46.00 | 71.09 | 94.30 | 16.25 | 78.05 |
| ZS0‐2 | 48 120 716 | 42 194 592 | 12.32 | 47.00 | 69.59 | 94.80 | 14.40 | 80.40 |
| ZS0‐3 | 42 576 320 | 38 432 417 | 9.73 | 47.00 | 64.92 | 94.80 | 12.16 | 82.64 |
| ZS12‐1 | 45 354 078 | 39 798 395 | 12.25 | 46.00 | 65.65 | 93.00 | 15.01 | 77.99 |
| ZS12‐2 | 44 975 674 | 39 552 394 | 12.06 | 47.00 | 74.07 | 91.50 | 15.01 | 76.49 |
| ZS24‐1 | 53 669 230 | 47 363 672 | 11.75 | 46.00 | 67.07 | 92.70 | 16.06 | 76.64 |
| ZS24‐2 | 55 131 416 | 49 939 119 | 9.42 | 44.00 | 63.38 | 93.30 | 16.11 | 77.19 |
| ZS24‐3 | 41 023 534 | 36 764 413 | 10.38 | 47.00 | 67.66 | 95.80 | 11.29 | 84.51 |
| ZS48‐1 | 44 327 802 | 40 192 320 | 9.33 | 44.00 | 65.26 | 90.90 | 14.23 | 76.67 |
| ZS48‐2 | 45 137 982 | 40 979 051 | 9.21 | 44.00 | 63.40 | 91.20 | 14.50 | 76.70 |