Table 2.
Categorization and abundance of tags
| Summary | L1 | L2 | L3 | L4 | L5 | L6 | L7 | L8 | |
|---|---|---|---|---|---|---|---|---|---|
| Raw tag | Total | 5986157 | 6040684 | 5895889 | 6168748 | 5865045 | 6216559 | 6198321 | 6131056 |
| Distinct tag | 466332 | 351691 | 351724 | 375846 | 591374 | 504549 | 519273 | 525066 | |
| Clean tag | Total number | 5739999 | 5846807 | 5731901 | 5970775 | 5476878 | 5900343 | 5930716 | 5862642 |
| Distinct tag number | 224154 | 162415 | 191994 | 181792 | 204639 | 206998 | 233839 | 257077 | |
| All Tag Mapping to Gene | Total number | 4801389 | 4749586 | 5060517 | 5106678 | 4461094 | 4703005 | 4633630 | 4622199 |
| Total % of clean tag | 83.65% | 82.86% | 86.55% | 85.53% | 81.45% | 79.71% | 78.13% | 78.84% | |
| Distinct Tag number | 106706 | 97198 | 101471 | 103126 | 109186 | 115835 | 113282 | 120719 | |
| Distinct Tag % of clean tag | 47.60% | 50.63% | 62.48% | 56.73% | 53.36% | 55.96% | 48.44% | 46.96% | |
| Total number | 3292723 | 3227948 | 3507713 | 3554706 | 3256090 | 3434881 | 3343733 | 3402403 | |
| Total % of clean tag | 57.36% | 56.32% | 59.99% | 59.54% | 59.45% | 58.21% | 56.38% | 58.04% | |
| Unambiguous Tag Mapping to Gene | Distinct Tag number | 81596 | 75187 | 78233 | 79048 | 83632 | 88491 | 86619 | 92556 |
| Distinct Tag % of clean tag | 36.40% | 39.16% | 48.17% | 43.48% | 40.87% | 42.75% | 37.04% | 36.00% | |
| number | 37582 | 36093 | 35450 | 35798 | 37001 | 36554 | 36752 | 38802 | |
| % of ref genes | 56.76% | 54.51% | 53.54% | 54.07% | 55.88% | 55.21% | 55.51% | 58.60% | |
| All Tag-mapped Genes | number | 29503 | 28271 | 27960 | 27977 | 29174 | 28799 | 29217 | 30581 |
| % of ref genes | 44.56% | 42.70% | 42.23% | 42.25% | 44.06% | 43.50% | 44.13% | 46.19% | |
| Unambiguous Tag-mapped Genes | Total number | 271 | 460 | 131 | 180 | 567 | 396 | 434 | 626 |
| Total % of clean tag | 0.00% | 0.01% | 0.00% | 0.00% | 0.01% | 0.01% | 0.01% | 0.01% | |
| Mapping to Mitochondrion | Distinct Tag number | 39 | 44 | 25 | 32 | 57 | 41 | 38 | 68 |
| Distinct Tag % of clean tag | 0.02% | 0.02% | 0.02% | 0.02% | 0.03% | 0.02% | 0.02% | 0.03% | |
| Total number | 55363 | 40659 | 19740 | 21626 | 7022 | 6884 | 5876 | 7903 | |
| Total % of clean tag | 0.96% | 0.71% | 0.34% | 0.36% | 0.13% | 0.12% | 0.10% | 0.13% | |
| Mapping to Chloroplast | Distinct Tag number | 580 | 509 | 387 | 478 | 357 | 348 | 284 | 379 |
| Distinct Tag % of clean tag | 0.26% | 0.27% | 0.24% | 0.26% | 0.17% | 0.17% | 0.12% | 0.15% | |
| Total number | 556745 | 583356 | 494737 | 541514 | 547827 | 615239 | 579952 | 689884 | |
| Total % of clean tag | 9.70% | 10.18% | 8.46% | 9.07% | 10.00% | 10.43% | 9.78% | 11.77% | |
| Mapping to Genome | Distinct Tag number | 76405 | 59263 | 38836 | 48896 | 47539 | 44830 | 45655 | 77752 |
| Distinct Tag % of clean tag | 34.09% | 30.87% | 23.91% | 26.90% | 23.23% | 21.66% | 19.52% | 30.24% | |
| Total number | 326231 | 357840 | 271682 | 300777 | 460368 | 574819 | 710824 | 542030 | |
| Total % of clean tag | 5.68% | 6.24% | 4.65% | 5.04% | 8.41% | 9.74% | 11.99% | 9.25% | |
| Unknown Tag | Distinct Tag number | 40424 | 34980 | 21696 | 29260 | 47500 | 45944 | 74580 | 58159 |
| Distinct Tag % of clean tag | 18.03% | 18.22% | 13.36% | 16.10% | 23.21% | 22.20% | 31.89% | 22.62% |
Clean tags are those remaining after low quality tags have been removed from the raw data. Distinct tags are different kinds of tags. Unambiguous tags are the clean tags remaining after removal of tags mapped to reference sequences from multiple genes.