Table 2.
Distribution of mycelia small RNAs with perfect map to nuclear and mitochondria genomes.
| Alignmenta | Read Countb | Proratedc | Featuresd | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total | Sense | Antisense | Total | Sense | Antisense | Total | Sense | Antisense | Mapped | Total | Coverage | |
| Genome | 386741 | 211969 | 158036 | 32518 | 28592 | 6657 | 31985 | 26267 | 3569 | 3448 | 14880 | 23% |
| Genes | 41318 | 23046 | 20923 | 8459 | 6213 | 5095 | 4226 | 2522 | 1704 | 1156 | 11043 | 10% |
| Introns | 5396 | 3577 | 1821 | 1890 | 1848 | 263 | 209 | 191 | 17 | 121 | 19651 | 1% |
| Exons | 36860 | 20202 | 19302 | 8270 | 5702 | 5075 | 4017 | 2331 | 1686 | 1200 | 30705 | 4% |
| 5' UTRe | 11416 | 5020 | 6505 | 4907 | 3147 | 3204 | 2103 | 971 | 1132 | 223 | 11241 | 2% |
| EST Supp. | 3337 | 1715 | 1729 | 1151 | 502 | 844 | 691 | 100 | 590 | 83 | 2558 | 3% |
| Unsupp. | 8079 | 3306 | 4777 | 3955 | 2760 | 2496 | 1412 | 870 | 542 | 151 | 8683 | 2% |
| CDS | 4111 | 2959 | 1154 | 2463 | 2170 | 422 | 887 | 800 | 87 | 720 | 30486 | 2% |
| EST Supp. | 2607 | 1636 | 973 | 1177 | 930 | 354 | 686 | 628 | 58 | 561 | 18154 | 3% |
| Unsupp. | 1504 | 1324 | 182 | 1406 | 1302 | 136 | 201 | 172 | 29 | 159 | 12332 | 1% |
| 3' UTR | 23571 | 13686 | 12378 | 4347 | 3253 | 3342 | 1027 | 560 | 467 | 342 | 11076 | 3% |
| EST Supp. | 3609 | 1882 | 1777 | 662 | 603 | 315 | 218 | 170 | 48 | 156 | 2551 | 6% |
| Unsupp. | 19962 | 11805 | 10602 | 3921 | 2870 | 3243 | 810 | 390 | 419 | 198 | 8525 | 2% |
| tRNAf | 30934 | 25184 | 5752 | 5555 | 5468 | 89 | 4018 | 3983 | 35 | 338 | 341 | 99% |
| 5' Leader | 2020 | 1975 | 47 | 1494 | 1452 | 44 | 375 | 375 | 0 | 112 | 341 | 33% |
| Mature | 19615 | 19336 | 281 | 4243 | 4241 | 4 | 3137 | 3134 | 2 | 338 | 341 | 99% |
| 3' Term | 12937 | 7510 | 5429 | 1841 | 1799 | 44 | 506 | 474 | 32 | 209 | 341 | 61% |
| rRNA | 67781 | 67765 | 18 | 19559 | 19550 | 11 | 18197 | 18188 | 9 | 48 | 48 | 100% |
| 5.8 S | 1630 | 1630 | 1 | 950 | 950 | 1 | 950 | 950 | 0 | 3 | 3 | 100% |
| 8 S | 36761 | 36761 | 1 | 1141 | 1141 | 1 | 804 | 804 | 0 | 41 | 41 | 100% |
| 18 S | 5185 | 5183 | 4 | 5185 | 5183 | 4 | 4242 | 4240 | 2 | 2 | 2 | 100% |
| 28 S | 24205 | 24192 | 15 | 12283 | 12277 | 8 | 12201 | 12194 | 7 | 2 | 2 | 100% |
| snRNA | 162 | 162 | 1 | 129 | 129 | 1 | 90 | 90 | 0 | 8 | 14 | 57% |
| Transposable Elements | 248528 | 113951 | 134620 | 3369 | 1522 | 1883 | 3305 | 1484 | 1821 | 1898 | 3448 | 55% |
| Intergenic | 35342 | - | - | 4175 | - | - | 2150 | - | - | - | - | - |
| Mitochondria | 1448 | 1423 | 13 | 1445 | 1422 | 13 | 912 | 886 | 10 | 36 | 37 | 97% |
| Genes | 961 | 950 | 13 | 961 | 950 | 13 | 216 | 206 | 10 | 15 | 15 | 100% |
| CDS | 17 | 17 | 1 | 17 | 17 | 1 | 16 | 16 | 0 | 7 | 16 | 44% |
| tRNA | 1074 | 1074 | 1 | 1073 | 1073 | 1 | 464 | 464 | 0 | 18 | 20 | 90% |
| Mature | 346 | 346 | 1 | 345 | 345 | 1 | 107 | 107 | 0 | 18 | 20 | 90% |
| rRNA | 314 | 314 | 1 | 314 | 314 | 1 | 216 | 216 | 0 | 2 | 2 | 100% |
| Intergenic | 18 | - | - | 18 | - | - | 16 | - | - | - | - | - |
a Alignment refers to the summation of small RNA alignments to any genomic feature.
b Read Count represents the summation of distinct reads mapping to a given feature. Noteworthy the values for each genome feature are generally less than the sum of its sub-features due to the small RNAs mapping to multiple features (See "Material and Methods" for more details).
c Prorated apportions the weight of any small RNA between alignments and features.
d Features represent the proportion of genomic features mapped by small RNAs where mapped indicates the number of members for each genomic feature mapped by small RNAs among the total possible.
e Values indicate number of small RNAs that mapped to sub-features within gene models that are supported by ESTs (EST Supp.) or have no EST supporting evidence (Unsupp.)
f tRNA entries include pseudo-tRNAs.