Statistics on ncRNA trees
ncRNA trees
Since release 58, Compara computes phylogenetic trees for the non-coding RNAs annotating by RFAM. The manuscript is in preparation. More information can be obtained here
- Gene coverage: Number of genes and members in total, included in trees (either species-specific, or encompassing other species), and orphaned (not in any tree)
- Tree size: Sizes of trees (genes, and distinct species), grouped according to the root ancestral species
- Predicted gene events: For each ancestral species, number of speciation and duplication nodes (inc. dubious ones), with the average duplication score
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Number of genes and members in total, included in trees (either species-specific, or encompassing other species), and orphaned (not in any tree)
taxon_id | taxon_name | nb_trans | nb_canon_trans | nb_trans_spectree | nb_trans_anctree | nb_trans_orphan | perc_trans_spectree | perc_trans_anctree | perc_trans_orphan |
---|---|---|---|---|---|---|---|---|---|
7757 | Petromyzon marinus | 2628 | 2628 | 0 | 68 | 2560 | 0.00 | 2.59 | 97.41 |
7897 | Latimeria chalumnae | 2918 | 2918 | 0 | 367 | 2551 | 0.00 | 12.58 | 87.42 |
28377 | Anolis carolinensis | 3160 | 3160 | 6 | 821 | 2333 | 0.19 | 25.98 | 73.83 |
9103 | Meleagris gallopavo | 756 | 756 | 0 | 410 | 346 | 0.00 | 54.23 | 45.77 |
9031 | Gallus gallus | 1102 | 1102 | 0 | 242 | 860 | 0.00 | 21.96 | 78.04 |
59729 | Taeniopygia guttata | 724 | 724 | 0 | 467 | 257 | 0.00 | 64.50 | 35.50 |
9258 | Ornithorhynchus anatinus | 3871 | 3871 | 0 | 556 | 3315 | 0.00 | 14.36 | 85.64 |
9361 | Dasypus novemcinctus | 4475 | 4475 | 0 | 102 | 4373 | 0.00 | 2.28 | 97.72 |
9358 | Choloepus hoffmanni | 2030 | 2030 | 0 | 72 | 1958 | 0.00 | 3.55 | 96.45 |
37347 | Tupaia belangeri | 3049 | 3049 | 0 | 234 | 2815 | 0.00 | 7.67 | 92.33 |
10020 | Dipodomys ordii | 3036 | 3036 | 0 | 135 | 2901 | 0.00 | 4.45 | 95.55 |
10090 | Mus musculus | 8538 | 7543 | 0 | 2619 | 4924 | 0.00 | 34.72 | 65.28 |
10116 | Rattus norvegicus | 4828 | 4828 | 0 | 1456 | 3372 | 0.00 | 30.16 | 69.84 |
43179 | Ictidomys tridecemlineatus | 3166 | 3166 | 0 | 670 | 2496 | 0.00 | 21.16 | 78.84 |
10141 | Cavia porcellus | 5963 | 5963 | 0 | 170 | 5793 | 0.00 | 2.85 | 97.15 |
9978 | Ochotona princeps | 5708 | 5708 | 0 | 111 | 5597 | 0.00 | 1.94 | 98.06 |
9986 | Oryctolagus cuniculus | 3375 | 3375 | 0 | 155 | 3220 | 0.00 | 4.59 | 95.41 |
9478 | Tarsius syrichta | 5362 | 5362 | 0 | 109 | 5253 | 0.00 | 2.03 | 97.97 |
9544 | Macaca mulatta | 6579 | 6579 | 0 | 2625 | 3954 | 0.00 | 39.90 | 60.10 |
9601 | Pongo abelii | 6996 | 6996 | 0 | 2825 | 4171 | 0.00 | 40.38 | 59.62 |
9598 | Pan troglodytes | 8657 | 8657 | 0 | 5262 | 3395 | 0.00 | 60.78 | 39.22 |
9606 | Homo sapiens | 18406 | 14652 | 6 | 4223 | 10423 | 0.04 | 28.82 | 71.14 |
9593 | Gorilla gorilla | 6701 | 6701 | 0 | 2763 | 3938 | 0.00 | 41.23 | 58.77 |
61853 | Nomascus leucogenys | 7172 | 7172 | 0 | 386 | 6786 | 0.00 | 5.38 | 94.62 |
9483 | Callithrix jacchus | 9000 | 9000 | 0 | 5842 | 3158 | 0.00 | 64.91 | 35.09 |
30611 | Otolemur garnettii | 7276 | 7276 | 0 | 182 | 7094 | 0.00 | 2.50 | 97.50 |
30608 | Microcebus murinus | 7111 | 7111 | 0 | 153 | 6958 | 0.00 | 2.15 | 97.85 |
132908 | Pteropus vampyrus | 4171 | 4171 | 0 | 309 | 3862 | 0.00 | 7.41 | 92.59 |
59463 | Myotis lucifugus | 4408 | 4408 | 0 | 329 | 4079 | 0.00 | 7.46 | 92.54 |
9685 | Felis catus | 2930 | 2930 | 0 | 122 | 2808 | 0.00 | 4.16 | 95.84 |
9646 | Ailuropoda melanoleuca | 3141 | 3141 | 0 | 183 | 2958 | 0.00 | 5.83 | 94.17 |
9615 | Canis familiaris | 3613 | 3613 | 0 | 1101 | 2512 | 0.00 | 30.47 | 69.53 |
9796 | Equus caballus | 2118 | 2118 | 0 | 804 | 1314 | 0.00 | 37.96 | 62.04 |
42254 | Sorex araneus | 4558 | 4558 | 0 | 83 | 4475 | 0.00 | 1.82 | 98.18 |
9365 | Erinaceus europaeus | 6432 | 6432 | 0 | 101 | 6331 | 0.00 | 1.57 | 98.43 |
30538 | Vicugna pacos | 2508 | 2508 | 0 | 96 | 2412 | 0.00 | 3.83 | 96.17 |
9823 | Sus scrofa | 2989 | 2989 | 0 | 1412 | 1577 | 0.00 | 47.24 | 52.76 |
9913 | Bos taurus | 3825 | 3825 | 0 | 811 | 3014 | 0.00 | 21.20 | 78.80 |
9739 | Tursiops truncatus | 3766 | 3766 | 0 | 168 | 3598 | 0.00 | 4.46 | 95.54 |
9785 | Loxodonta africana | 2644 | 2644 | 0 | 341 | 2303 | 0.00 | 12.90 | 87.10 |
9813 | Procavia capensis | 1696 | 1696 | 0 | 239 | 1457 | 0.00 | 14.09 | 85.91 |
9371 | Echinops telfairi | 5656 | 5656 | 0 | 109 | 5547 | 0.00 | 1.93 | 98.07 |
13616 | Monodelphis domestica | 1850 | 1850 | 0 | 517 | 1333 | 0.00 | 27.95 | 72.05 |
9305 | Sarcophilus harrisii | 1490 | 1490 | 0 | 709 | 781 | 0.00 | 47.58 | 52.42 |
9315 | Macropus eugenii | 1472 | 1472 | 0 | 597 | 875 | 0.00 | 40.56 | 59.44 |
8364 | Xenopus tropicalis | 1282 | 1282 | 0 | 474 | 808 | 0.00 | 36.97 | 63.03 |
99883 | Tetraodon nigroviridis | 813 | 813 | 0 | 354 | 459 | 0.00 | 43.54 | 56.46 |
31033 | Takifugu rubripes | 703 | 703 | 0 | 325 | 378 | 0.00 | 46.23 | 53.77 |
69293 | Gasterosteus aculeatus | 1617 | 1617 | 0 | 604 | 1013 | 0.00 | 37.35 | 62.65 |
8090 | Oryzias latipes | 735 | 735 | 0 | 296 | 439 | 0.00 | 40.27 | 59.73 |
8128 | Oreochromis niloticus | 821 | 821 | 0 | 487 | 334 | 0.00 | 59.32 | 40.68 |
8049 | Gadus morhua | 1541 | 1541 | 0 | 371 | 1170 | 0.00 | 24.08 | 75.92 |
7955 | Danio rerio | 4598 | 4556 | 0 | 1264 | 3292 | 0.00 | 27.74 | 72.26 |
7719 | Ciona intestinalis | 455 | 455 | 0 | 34 | 421 | 0.00 | 7.47 | 92.53 |
51511 | Ciona savignyi | 314 | 314 | 0 | 118 | 196 | 0.00 | 37.58 | 62.42 |
7227 | Drosophila melanogaster | 1031 | 970 | NULL | 0 | NULL | NULL | 0.00 | NULL |
6239 | Caenorhabditis elegans | 23655 | 23650 | NULL | 0 | NULL | NULL | 0.00 | NULL |
4932 | Saccharomyces cerevisiae | 413 | 413 | NULL | 0 | NULL | NULL | 0.00 | NULL |
Total | 239832 | 234975 | 12 | 45383 | 189580 | 0.01 | 19.31 | 80.68 |
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Sizes of trees (genes, and distinct species), grouped according to the root ancestral species
taxon_id | taxon_name | nb_trees | tot_nb_trans | avg_nb_trans | max_nb_trans | avg_nb_spec | max_nb_spec | avg_nb_trans_per_spec |
---|---|---|---|---|---|---|---|---|
7711 | Chordata | 30 | 13594 | 453.13 | 3828 | 41.47 | 54 | 12.76 |
7742 | Vertebrata | 33 | 3770 | 114.24 | 753 | 42.79 | 53 | 2.69 |
117571 | Euteleostomi | 176 | 17335 | 98.49 | 5412 | 18.35 | 51 | 5.90 |
8287 | Sarcopterygii | 7 | 217 | 31.00 | 43 | 28.57 | 42 | 1.15 |
32523 | Tetrapoda | 6 | 328 | 54.67 | 147 | 36.33 | 40 | 1.46 |
32524 | Amniota | 61 | 1240 | 20.33 | 93 | 11.15 | 40 | 1.93 |
28377 | Anolis carolinensis | 1 | 6 | 6.00 | 6 | 1.00 | 1 | 6.00 |
40674 | Mammalia | 10 | 345 | 34.50 | 112 | 25.50 | 39 | 1.25 |
32525 | Theria | 23 | 2948 | 128.17 | 2285 | 10.65 | 29 | 15.00 |
9347 | Eutheria | 156 | 5606 | 35.94 | 750 | 14.30 | 35 | 2.76 |
9606 | Homo sapiens | 1 | 6 | 6.00 | 6 | 1.00 | 1 | 6.00 |
Total | 504 | 45395 | 90.07 | 5412 | 19.28 | 54 | 4.85 |
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For each ancestral species, number of speciation and duplication nodes (inc. dubious ones), with the average duplication score
taxon_id | taxon_name | nb_nodes | nb_spec_nodes | nb_dup_nodes | nb_dubious_nodes | nb_gene_splits | avg_dupscore | avg_dupscore_nondub |
---|---|---|---|---|---|---|---|---|
7711 | Chordata | 139 | 34 | 95 | 10 | 0 | 0.38 | 0.38 |
7742 | Vertebrata | 136 | 64 | 69 | 3 | 0 | 0.34 | 0.34 |
7757 | Petromyzon marinus | 2 | 0 | 2 | 0 | 0 | 1.00 | 1.00 |
117571 | Euteleostomi | 1969 | 528 | 1109 | 332 | 0 | 0.23 | 0.23 |
8287 | Sarcopterygii | 588 | 230 | 270 | 88 | 0 | 0.35 | 0.35 |
7897 | Latimeria chalumnae | 70 | 0 | 70 | 0 | 0 | 1.00 | 1.00 |
32523 | Tetrapoda | 349 | 166 | 105 | 78 | 0 | 0.32 | 0.32 |
32524 | Amniota | 1527 | 602 | 624 | 301 | 0 | 0.31 | 0.31 |
32561 | Sauria | 740 | 710 | 30 | 0 | 0 | 0.66 | 0.66 |
28377 | Anolis carolinensis | 269 | 0 | 269 | 0 | 0 | 1.00 | 1.00 |
9103 | Meleagris gallopavo | 11 | 0 | 11 | 0 | 0 | 1.00 | 1.00 |
9031 | Gallus gallus | 12 | 0 | 12 | 0 | 0 | 1.00 | 1.00 |
59729 | Taeniopygia guttata | 80 | 0 | 80 | 0 | 0 | 1.00 | 1.00 |
40674 | Mammalia | 455 | 225 | 126 | 104 | 0 | 0.30 | 0.30 |
9258 | Ornithorhynchus anatinus | 200 | 0 | 200 | 0 | 0 | 1.00 | 1.00 |
32525 | Theria | 1278 | 539 | 562 | 177 | 0 | 0.37 | 0.37 |
9347 | Eutheria | 28982 | 22258 | 6724 | 0 | 0 | 0.55 | 0.55 |
37347 | Tupaia belangeri | 10 | 0 | 10 | 0 | 0 | 1.00 | 1.00 |
10020 | Dipodomys ordii | 2 | 0 | 2 | 0 | 0 | 1.00 | 1.00 |
10090 | Mus musculus | 1152 | 0 | 1152 | 0 | 0 | 1.00 | 1.00 |
10116 | Rattus norvegicus | 166 | 0 | 166 | 0 | 0 | 1.00 | 1.00 |
43179 | Ictidomys tridecemlineatus | 20 | 0 | 20 | 0 | 0 | 1.00 | 1.00 |
10141 | Cavia porcellus | 2 | 0 | 2 | 0 | 0 | 1.00 | 1.00 |
9978 | Ochotona princeps | 1 | 0 | 1 | 0 | 0 | 1.00 | 1.00 |
9478 | Tarsius syrichta | 1 | 0 | 1 | 0 | 0 | 1.00 | 1.00 |
9544 | Macaca mulatta | 123 | 0 | 123 | 0 | 0 | 1.00 | 1.00 |
9601 | Pongo abelii | 187 | 0 | 187 | 0 | 0 | 1.00 | 1.00 |
9598 | Pan troglodytes | 451 | 0 | 451 | 0 | 0 | 1.00 | 1.00 |
9606 | Homo sapiens | 78 | 0 | 78 | 0 | 0 | 1.00 | 1.00 |
9593 | Gorilla gorilla | 105 | 0 | 105 | 0 | 0 | 1.00 | 1.00 |
61853 | Nomascus leucogenys | 2 | 0 | 2 | 0 | 0 | 1.00 | 1.00 |
9483 | Callithrix jacchus | 1157 | 0 | 1157 | 0 | 0 | 1.00 | 1.00 |
30608 | Microcebus murinus | 1 | 0 | 1 | 0 | 0 | 1.00 | 1.00 |
132908 | Pteropus vampyrus | 7 | 0 | 7 | 0 | 0 | 1.00 | 1.00 |
59463 | Myotis lucifugus | 20 | 0 | 20 | 0 | 0 | 1.00 | 1.00 |
9615 | Canis familiaris | 84 | 0 | 84 | 0 | 0 | 1.00 | 1.00 |
9796 | Equus caballus | 34 | 0 | 34 | 0 | 0 | 1.00 | 1.00 |
42254 | Sorex araneus | 1 | 0 | 1 | 0 | 0 | 1.00 | 1.00 |
9365 | Erinaceus europaeus | 1 | 0 | 1 | 0 | 0 | 1.00 | 1.00 |
30538 | Vicugna pacos | 1 | 0 | 1 | 0 | 0 | 1.00 | 1.00 |
9823 | Sus scrofa | 289 | 0 | 289 | 0 | 0 | 1.00 | 1.00 |
9913 | Bos taurus | 39 | 0 | 39 | 0 | 0 | 1.00 | 1.00 |
9785 | Loxodonta africana | 20 | 0 | 20 | 0 | 0 | 1.00 | 1.00 |
9813 | Procavia capensis | 4 | 0 | 4 | 0 | 0 | 1.00 | 1.00 |
9263 | Marsupialia | 705 | 615 | 90 | 0 | 0 | 0.61 | 0.61 |
13616 | Monodelphis domestica | 60 | 0 | 60 | 0 | 0 | 1.00 | 1.00 |
9305 | Sarcophilus harrisii | 73 | 0 | 73 | 0 | 0 | 1.00 | 1.00 |
9315 | Macropus eugenii | 36 | 0 | 36 | 0 | 0 | 1.00 | 1.00 |
8364 | Xenopus tropicalis | 242 | 0 | 242 | 0 | 0 | 1.00 | 1.00 |
186625 | Clupeocephala | 1502 | 1342 | 160 | 0 | 0 | 0.51 | 0.51 |
99883 | Tetraodon nigroviridis | 94 | 0 | 94 | 0 | 0 | 1.00 | 1.00 |
31033 | Takifugu rubripes | 48 | 0 | 48 | 0 | 0 | 1.00 | 1.00 |
69293 | Gasterosteus aculeatus | 212 | 0 | 212 | 0 | 0 | 1.00 | 1.00 |
8090 | Oryzias latipes | 35 | 0 | 35 | 0 | 0 | 1.00 | 1.00 |
8128 | Oreochromis niloticus | 57 | 0 | 57 | 0 | 0 | 1.00 | 1.00 |
8049 | Gadus morhua | 110 | 0 | 110 | 0 | 0 | 1.00 | 1.00 |
7955 | Danio rerio | 835 | 0 | 835 | 0 | 0 | 1.00 | 1.00 |
7718 | Ciona | 55 | 27 | 28 | 0 | 0 | 0.59 | 0.59 |
7719 | Ciona intestinalis | 3 | 0 | 3 | 0 | 0 | 1.00 | 1.00 |
51511 | Ciona savignyi | 59 | 0 | 59 | 0 | 0 | 1.00 | 1.00 |
Total (ancestral species) | 38425 | 27340 | 9992 | 1093 | 0 | 0.48 | 0.48 | |
Total (extant species) | 6466 | 0 | 6466 | 0 | 0 | 1.00 | 1.00 | |
Total | 44891 | 27340 | 16458 | 1093 | 0 | 0.68 | 0.68 |