Table 1 Mapping distribution of the clean reads in small RNA libraries
Categories | Vandana | Aday Sel | IR64 | |||
|---|---|---|---|---|---|---|
Total reads | Unique reads | Total reads | Unique reads | Total reads | Unique reads | |
Clean reads | 16 847 232 ± 1 528 242 | 3 332 304 ± 635 063 | 15 403 441 ± 1 282 332 | 2 394 590 ± 675 288 | 18 622 662 ± 1 208 043 | 3 643 737 ± 1 094 125 |
9311 rice genome | 10 249 097 ± 1 228 933 (60.8 %) | 1 480 850 ± 296 597 (44.4 %) | 10 647 829 ± 1 682 873 (69.1 %) | 793 346 ± 194 986 (33.1 %) | 13 818 525 ± 2 320 473 (74.2 %) | 1 614 944 ± 469 863 (44.3 %) |
Exon antisense | 123 658 ± 31 951 (0.7 %) | 37 913 ± 10 407 (1.1 %) | 143 789 ± 58 608 (0.9 %) | 29 918 ± 8184 (1.3 %) | 135 144 ± 31 018 (0.7 %) | 43 449 ± 9513 (1.2 %) |
Exon sense | 148 224 ± 44 300 (0.9 %) | 84 852 ± 23 724 (2.6 %) | 159 436 ± 46 424 (1.0 %) | 80 885 ± 14 721 (3.4 %) | 184 756 ± 32 941 (1.0 %) | 85 802 ± 26 065 (2.4 %) |
Intron antisense | 115 867 ± 30 826 (0.7 %) | 50 016 ± 10 263 (1.5 %) | 50 944 ± 20 434 (0.3 %) | 26 964 ± 7620 (1.1 %) | 132 987 ± 40 799 (0.7 %) | 55 629 ± 15 460 (1.5 %) |
Intron sense | 188 761 ± 62 005 (1.1 %) | 58 543 ± 12 020 (1.8 %) | 83 925 ± 30 603 (0.5 %) | 33 330 ± 8440 (1.4 %) | 182 440 ± 36 679 (1.0 %) | 62 038 ± 15 960 (1.7 %) |
Known miRNA | 4 457 106 ± 1 511 316 (26.5 %) | 6037 ± 490 (0.2 %) | 6 769 286 ± 1 144 378 (44.0 %) | 5598 ± 985 (0.2 %) | 5 404 163 ± 2 597 947 (29.0 %) | 5759 ± 556 (0.2 %) |
rRNA | 1 046 140 ± 299 191 (6.2 %) | 77 037 ± 12 331 (2.3 %) | 1 785 015 ± 239 128 (11.6 %) | 102 438 ± 13 644 (4.3 %) | 699 723 ± 182 679 (3.8 %) | 65 568 ± 9341 (1.8 %) |
Repeat | 2 433 147 ± 506 069 (14.4 %) | 1 005 986 ± 166 997 (30.2 %) | 1 547 941 ± 684 735 (10.1 %) | 666 553 ± 189 898 (27.8 %) | 2 609 401 ± 865 194 (14.0 %) | 1 029 967 ± 288 440 (28.3 %) |
snRNA | 10 215 ± 4326 (0.1 %) | 2250 ± 489 (0.1 %) | 17 203 ± 1154 (0.1 %) | 3136 ± 391 (0.1 %) | 5920 ± 907 (0.0 %) | 1566 ± 175 (0.0 %) |
snoRNA | 18 859 ± 5210 (0.1 %) | 3261 ± 677 (0.1 %) | 9806 ± 2330 (0.1 %) | 2986 ± 598 (0.1 %) | 9433 ± 2721 (0.1 %) | 2816 ± 263 (0.1 %) |
tRNA | 2 428 011 ± 1 192 154 (14.4 %) | 18 784 ± 3404 (0.6 %) | 2 035 604 ± 2 480 765 (13.2 %) | 18 371 ± 3104 (0.8 %) | 4 904 192 ± 5 445 456 (26.3 %) | 17 397 ± 3844 (0.5 %) |
Unannotated | 5 877 246 ± 1 887 347 (34.9 %) | 1 987 625 ± 398 270 (59.7 %) | 2 800 494 ± 1 023 410 (18.2 %) | 1 424 411 ± 473 219 (59.5 %) | 4 354 504 ± 1 328 748 (23.4 %) | 2 273 749 ± 737 311 (62.4 %) |