TransRate contents for Arabidopsis thaliana
S6.1: TransRate results for Arabidopsis thaliana assemblies
Scores and read-based metrics can only be calculated for paired-end data. This data set consists of single-end data.
| assembly | n_seqs | smallest | largest | n_bases | mean_len | n_under_200 | n_over_1k | n_over_10k | n_with_orf | mean_orf_percent | n90 | n70 | n50 | n30 |
|---|
| trinity | 34617 | 201 | 10819 | 35964287 | 1038.91981 | 0 | 13342 | 2 | 19270 | 74.79009 | 459 | 1032 | 1576 | 2213 |
| oases | 57809 | 101 | 14892 | 78762767 | 1355.39494 | 2723 | 32622 | 23 | 41459 | 72.07497 | 770 | 1335 | 1832 | 2526 |
| trans-abyss | 66004 | 100 | 9650 | 53180949 | 766.50761 | 19819 | 19689 | 0 | 26933 | 72.50447 | 545 | 1124 | 1653 | 2350 |
| soap-trans-default | 50876 | 100 | 7576 | 28632860 | 513.59853 | 18627 | 8697 | 0 | 15449 | 80.77778 | 369 | 803 | 1318 | 2016 |
| rna-spades | 36953 | 49 | 8674 | 30621356 | 797.35318 | 6606 | 11146 | 0 | 15804 | 75.67217 | 427 | 1040 | 1578 | 2190 |
| spades | 29929 | 55 | 10645 | 29569509 | 980.87477 | 1659 | 11159 | 1 | 15323 | 74.47182 | 451 | 1096 | 1638 | 2261 |
| idba-tran | 32447 | 200 | 10599 | 27666394 | 852.66416 | 0 | 9564 | 1 | 16230 | 80.70797 | 369 | 803 | 1282 | 1839 |
| bridger | 30017 | 201 | 10044 | 33008527 | 1099.66109 | 0 | 12874 | 1 | 17635 | 74.66313 | 523 | 1115 | 1628 | 2226 |
| binpacker | 5914 | 200 | 9766 | 9081798 | 1535.6439 | 0 | 3775 | 0 | 4510 | 66.83681 | 838 | 1375 | 1879 | 2617 |
| shannon | 27685 | 200 | 10604 | 30178020 | 1090.04949 | 0 | 12001 | 3 | 16495 | 76.08368 | 524 | 1116 | 1607 | 2176 |
| assembly | n10 | gc | bases_n | proportion_n | CRBB_hits | n_contigs_with_CRBB | p_contigs_with_CRBB | rbh_per_reference | n_refs_with_CRBB | p_refs_with_CRBB | cov25 | p_cov25 | cov50 | p_cov50 | cov75 |
|---|
| trinity | 3491 | 0.42463 | 0 | 0.0 | 31053 | 31053 | 0.89704 | 0.64213 | 20829 | 0.43072 | 9275 | 0.19179 | 7209 | 0.14907 | 5317 |
| oases | 3945 | 0.42777 | 0 | 0.0 | 54291 | 54291 | 0.93914 | 1.12267 | 20281 | 0.41938 | 10802 | 0.22337 | 9454 | 0.1955 | 7372 |
| trans-abyss | 4091 | 0.42773 | 0 | 0.0 | 53643 | 53643 | 0.81272 | 1.10927 | 24186 | 0.50013 | 12529 | 0.25908 | 9882 | 0.20435 | 7142 |
| soap-trans-default | 4953 | 0.4242 | 0 | 0.0 | 40960 | 40960 | 0.80509 | 0.847 | 22266 | 0.46043 | 9353 | 0.19341 | 6404 | 0.13243 | 4032 |
| rna-spades | 3662 | 0.42403 | 500 | 2.0e-05 | 31615 | 31615 | 0.85555 | 0.65376 | 20578 | 0.42553 | 9195 | 0.19014 | 7147 | 0.14779 | 5109 |
| spades | 3585 | 0.4241 | 500 | 2.0e-05 | 26496 | 26496 | 0.8853 | 0.5479 | 19578 | 0.40485 | 8737 | 0.18067 | 7064 | 0.14607 | 5260 |
| idba-tran | 2955 | 0.42679 | 0 | 0.0 | 29438 | 29438 | 0.90726 | 0.60874 | 20089 | 0.41541 | 9180 | 0.18983 | 6714 | 0.13884 | 4372 |
| bridger | 3482 | 0.42512 | 0 | 0.0 | 26811 | 26811 | 0.89319 | 0.55442 | 19265 | 0.39837 | 7750 | 0.16026 | 6256 | 0.12937 | 4596 |
| binpacker | 4024 | 0.42792 | 0 | 0.0 | 5726 | 5726 | 0.96821 | 0.11841 | 4189 | 0.08662 | 1850 | 0.03826 | 1650 | 0.03412 | 1258 |
| shannon | 3355 | 0.42529 | 0 | 0.0 | 25053 | 25053 | 0.90493 | 0.51806 | 16671 | 0.34473 | 8601 | 0.17786 | 7175 | 0.14837 | 5550 |
| assembly | p_cov75 | cov85 | p_cov85 | cov95 | p_cov95 | reference_coverage | score | optimal_score | cutoff | weighted
|
|---|
| trinity | 0.10995 | 3848 | 0.07957 | 1194 | 0.02469 | 0.15512 | NA | NA | NA | NA
|
| oases | 0.15244 | 5389 | 0.11144 | 1623 | 0.03356 | 0.19207 | NA | NA | NA | NA
|
| trans-abyss | 0.14769 | 4926 | 0.10186 | 1190 | 0.02461 | 0.20992 | NA | NA | NA | NA
|
| soap-trans-default | 0.08338 | 2583 | 0.05341 | 630 | 0.01303 | 0.1479 | NA | NA | NA | NA
|
| rna-spades | 0.10565 | 3691 | 0.07632 | 1049 | 0.02169 | 0.15415 | NA | NA | NA | NA
|
| spades | 0.10877 | 3890 | 0.08044 | 1137 | 0.02351 | 0.151 | NA | NA | NA | NA
|
| idba-tran | 0.09041 | 2845 | 0.05883 | 626 | 0.01294 | 0.14613 | NA | NA | NA | NA
|
| bridger | 0.09504 | 3260 | 0.06741 | 955 | 0.01975 | 0.132 | NA | NA | NA | NA
|
| binpacker | 0.02601 | 850 | 0.01758 | 250 | 0.00517 | 0.03029 | NA | NA | NA | NA
|
| shannon | 0.11477 | 3997 | 0.08265 | 1099 | 0.02273 | 0.14777 | NA | NA | NA | NA
|