TransRate contents for Escherichia coli
S6.1: TransRate results for Escherichia coli 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 | 4403 | 201 | 17148 | 2143836 | 486.90347 | 0 | 347 | 3 | 927 | 75.0361 | 238 | 349 | 553 | 1014 |
| oases | 7364 | 100 | 15113 | 3602307 | 438.58446 | 2545 | 742 | 6 | 1526 | 65.71726 | 302 | 582 | 1051 | 2169 |
| trans-abyss | 9555 | 100 | 10359 | 3081448 | 247.63987 | 5101 | 445 | 3 | 1059 | 72.73044 | 263 | 483 | 1023 | 3220 |
| soap-trans-default | 7007 | 100 | 12363 | 2579222 | 302.57557 | 3225 | 439 | 1 | 998 | 71.98807 | 270 | 496 | 958 | 2244 |
| rna-spades | 7067 | 123 | 9580 | 2556747 | 298.58426 | 2730 | 340 | 0 | 888 | 73.77677 | 250 | 408 | 741 | 1679 |
| spades | 4119 | 56 | 12568 | 2370141 | 573.53484 | 80 | 488 | 1 | 1073 | 69.46914 | 261 | 438 | 758 | 1398 |
| idba-tran | 3803 | 200 | 12555 | 2069405 | 544.15067 | 0 | 414 | 1 | 949 | 71.99301 | 254 | 408 | 680 | 1208 |
| bridger | 4254 | 201 | 12772 | 2117305 | 497.72097 | 0 | 363 | 1 | 926 | 74.59062 | 238 | 361 | 582 | 1050 |
| binpacker | 157 | 207 | 12664 | 191067 | 1216.98726 | 0 | 66 | 1 | 66 | 45.13338 | 522 | 1169 | 1809 | 2739 |
| shannon | 4221 | 200 | 17145 | 2145566 | 508.30751 | 0 | 371 | 2 | 930 | 73.3447 | 240 | 367 | 598 | 1125 |
| 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 | 2652 | 0.51172 | 0 | 0.0 | 3396 | 3396 | 0.77129 | 0.78575 | 2283 | 0.52823 | 1827 | 0.42272 | 1296 | 0.29986 | 826 |
| oases | 15113 | 0.51132 | 0 | 0.0 | 5535 | 5535 | 0.75163 | 1.28066 | 2618 | 0.60574 | 1731 | 0.40051 | 1233 | 0.28528 | 758 |
| trans-abyss | 10359 | 0.50831 | 0 | 0.0 | 6353 | 6353 | 0.66489 | 1.46992 | 3038 | 0.70292 | 194 | 0.04489 | 61 | 0.01411 | 27 |
| soap-trans-default | 12363 | 0.51116 | 0 | 0.0 | 5127 | 5127 | 0.7317 | 1.18626 | 2984 | 0.69042 | 1190 | 0.27534 | 667 | 0.15433 | 373 |
| rna-spades | 9580 | 0.5098 | 200 | 8.0e-05 | 5140 | 5140 | 0.72732 | 1.18926 | 2968 | 0.68672 | 1135 | 0.26261 | 554 | 0.12818 | 281 |
| spades | 3287 | 0.51056 | 100 | 4.0e-05 | 3361 | 3361 | 0.81597 | 0.77765 | 2397 | 0.5546 | 876 | 0.20268 | 509 | 0.11777 | 283 |
| idba-tran | 2667 | 0.51303 | 0 | 0.0 | 3086 | 3086 | 0.81146 | 0.71402 | 2212 | 0.5118 | 969 | 0.2242 | 579 | 0.13397 | 343 |
| bridger | 2643 | 0.51242 | 0 | 0.0 | 3293 | 3293 | 0.77409 | 0.76192 | 2249 | 0.52036 | 1795 | 0.41532 | 1281 | 0.29639 | 810 |
| binpacker | 7479 | 0.50882 | 0 | 0.0 | 112 | 112 | 0.71338 | 0.02591 | 95 | 0.02198 | 35 | 0.0081 | 26 | 0.00602 | 21 |
| shannon | 3011 | 0.51234 | 0 | 0.0 | 3272 | 3272 | 0.77517 | 0.75706 | 2222 | 0.51411 | 1759 | 0.40699 | 1233 | 0.28528 | 779 |
| assembly | p_cov75 | cov85 | p_cov85 | cov95 | p_cov95 | reference_coverage | score | optimal_score | cutoff | weighted
|
|---|
| trinity | 0.19112 | 663 | 0.1534 | 530 | 0.12263 | 0.31635 | NA | NA | NA | NA
|
| oases | 0.17538 | 618 | 0.14299 | 490 | 0.11337 | 0.30558 | NA | NA | NA | NA
|
| trans-abyss | 0.00625 | 22 | 0.00509 | 15 | 0.00347 | 0.02844 | NA | NA | NA | NA
|
| soap-trans-default | 0.0863 | 298 | 0.06895 | 246 | 0.05692 | 0.19492 | NA | NA | NA | NA
|
| rna-spades | 0.06502 | 225 | 0.05206 | 187 | 0.04327 | 0.17587 | NA | NA | NA | NA
|
| spades | 0.06548 | 235 | 0.05437 | 193 | 0.04466 | 0.14391 | NA | NA | NA | NA
|
| idba-tran | 0.07936 | 296 | 0.06849 | 237 | 0.05484 | 0.16029 | NA | NA | NA | NA
|
| bridger | 0.18741 | 649 | 0.15016 | 520 | 0.12031 | 0.31082 | NA | NA | NA | NA
|
| binpacker | 0.00486 | 19 | 0.0044 | 18 | 0.00416 | 0.00619 | NA | NA | NA | NA
|
| shannon | 0.18024 | 641 | 0.14831 | 518 | 0.11985 | 0.3049 | NA | NA | NA | NA
|