Online-only Table 2.
Transrate and Busco statistics of the 16 initial liver transcriptome assemblies of S. scombrus.
| Basic statistics | Trinity | RnaSpades | SOAPdenovo-Trans (k25) | SOAPdenovo-Trans (k31) | SOAPdenovo-Trans (k41) | SOAPdenovo-Trans (k51) | SOAPdenovo-Trans (k61) | SOAPdenovo-Trans (k71) | SOAPdenovo-Trans (k81) | Idba-trans (k25) | Idba-trans (k31) | Idba-trans (k41) | Idba-trans (k51) | Idba-trans (k61) | Idba-trans (k71) | Idba-trans (k81) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Number of transcripts | 338127 | 232079 | 147977 | 150881 | 155364 | 161248 | 167990 | 157372 | 127912 | 158669 | 154159 | 156448 | 159617 | 162132 | 163995 | 164176 |
| Longest transcript | 44312 | 31456 | 24021 | 18568 | 28780 | 23475 | 22324 | 21718 | 25449 | 13982 | 15855 | 15411 | 22675 | 14708 | 17172 | 23031 |
| n bases | 332877922 | 177812586 | 110023758 | 112372948 | 111808036 | 110297592 | 107667878 | 101838468 | 91484534 | 93886615 | 97249133 | 97433311 | 96459740 | 94515627 | 92012738 | 88753661 |
| Mean transcript lenght (bp) | 984.48 | 766.17 | 743.52 | 744.78 | 719.65 | 684.02 | 640.92 | 647.12 | 715.21 | 591.71 | 630.84 | 622.78 | 604.32 | 582.95 | 561.07 | 540.6 |
| Number of transcripts over 1 K nt | 88423 | 38863 | 24989 | 25416 | 24927 | 24225 | 23147 | 22368 | 21502 | 20994 | 23006 | 22423 | 21489 | 20243 | 19132 | 17727 |
| Number of transcripts over 10 K nt | 566 | 306 | 183 | 186 | 206 | 180 | 143 | 122 | 98 | 10 | 24 | 22 | 21 | 25 | 29 | 23 |
| N90 trancript lenght (bp) | 356 | 279 | 273 | 271 | 261 | 248 | 241 | 250 | 275 | 272 | 276 | 273 | 268 | 262 | 253 | 246 |
| N70 trancript lenght (bp) | 921 | 553 | 582 | 584 | 557 | 516 | 465 | 464 | 531 | 454 | 485 | 472 | 450 | 427 | 405 | 386 |
| N50 trancript lenght (bp) | 1964 | 1610 | 1343 | 1361 | 1321 | 1256 | 1117 | 1107 | 1234 | 755 | 854 | 842 | 808 | 765 | 723 | 682 |
| N30 trancript lenght (bp) | 3346 | 3262 | 2852 | 2896 | 2843 | 2741 | 2507 | 2396 | 2496 | 1288 | 1517 | 1537 | 1505 | 1463 | 1408 | 1352 |
| N10 trancript lenght (bp) | 6008 | 6159 | 5886 | 5985 | 5934 | 5729 | 5279 | 5014 | 5014 | 2592 | 3140 | 3320 | 3272 | 3222 | 3107 | 3031 |
| Percentage of GC (%) | 0.44 | 0.43 | 0.43 | 0.43 | 0.43 | 0.43 | 0.43 | 0.43 | 0.44 | 0.43 | 0.43 | 0.43 | 0.43 | 0.43 | 0.43 | 0.43 |
| Busco analysis (%) | — | |||||||||||||||
| BUSCO Complete (Single + Duplicated)* | 97.03\97.34\80.78\72.45 | 92.74\93.35\73.05\64.18 | 97.03\96.22\78.96\70.64 | 96.37\96.01\78.23\70.88 | 96.04\95.60\77.49\70.07 | 95.05\94.99\77.30\68.59 | 94.06\93.87\72.89\65.34 | 91.09\92.33\92.33\64.11 | 91.42\90.80\68.64\61.21 | 63.04\65.13\38.86\31.22 | 63.04\66.67\40.56\34.23 | 64.36\66.56\40.64\34.21 | 64.03\69.63\42.38\35.73 | 69.97\74.13\44.97\37.85 | 72.94\77.10\47.72\40.29 | 76.90\79.14\49.57\41.97 |
| BUSCO Single* | 13.20\13.60\16.36\14.83 | 64.03\68.81\56.84\50.76 | 87.79\87.83\72.89\64.59 | 88.45\87.42\72.39\64.53 | 87.46\87.12\71.58\63.70 | 85.15\86.09\71.50\63.11 | 83.83\84.46\67.05\59.53 | 81.52\83.23\83.23\58.53 | 81.52\79.65\62.57\55.54 | 61.39\63.39\38.21\30.85 | 61.06\65.75\39.79\33.73 | 61.72\65.24\39.95\33.46 | 62.38\67.59\41.57\34.95 | 68.98\71.98\44.12\37.00 | 71.62\74.95\46.71\39.42 | 75.25\76.99\48.53\41.03 |
| BUSCO Duplicated* | 83.83\83.74\64.42\57.61 | 28.71\24.54\16.20\13.42 | 9.24\8.38\6.07\6.04 | 7.92\8.59\5.84\6.35 | 8.58\8.49\5.92\6.37 | 9.90\8.90\5.80\5.48 | 10.23\9.41\5.84\5.80 | 9.57\9.10\9.10\5.58 | 9.90\11.15\6.07\5.67 | 1.65\1.74\0.66\0.37 | 1.98\0.92\0.77\0.50 | 2.64\1.33\0.70\0.74 | 1.65\2.04\0.81\0.79 | 0.99\2.15\0.85\0.85 | 1.32\2.15\1.01\0.87 | 1.65\2.15\1.04\0.94 |
| BUSCO Fragmented* | 1.98\1.94\8.51\7.44 | 6.60\5.93\16.59\13.90 | 1.98\2.76\10.60\9.05 | 2.31\3.07\11.06\8.64 | 2.97\3.37\11.52\8.99 | 3.96\4.19\11.25\9.90 | 5.28\4.81\14.54\11.71 | 7.59\6.24\6.24\11.87 | 6.93\7.67\17.13\13.59 | 33.66\31.19\43.35\29.97 | 34.32\30.27\41.80\28.82 | 32.67\30.06\41.69\29.08 | 34.98\27.61\39.87\28.69 | 28.71\23.72\37.39\27.55 | 25.08\20.86\35.23\26.18 | 21.45\19.12\33.57\24.65 |
| BUSCO Missing* | 0.99\0.72\10.71\20.11 | 0.66\0.72\10.36\21.92 | 0.99\1.02\10.44\20.31 | 1.32\0.92\10.71\20.48 | 0.99\1.02\10.98\20.94 | 0.99\0.82\11.45\21.51 | 0.66\1.33\12.57\22.95 | 1.32\1.43\1.43\24.02 | 1.65\1.53\14.23\25.20 | 3.30\3.68\17.79\38.81 | 2.64\3.07\17.63\36.95 | 2.97\3.37\17.67\36.71 | 0.99\2.76\17.75\35.58 | 1.32\2.15\17.63\34.60 | 1.98\2.04\17.05\33.53 | 1.65\1.74\16.86\33.38 |
| Total Buscos Found* | 99.01\99.28\89.29\79.89 | 99.34\99.28\89.64\78.08 | 99.01\98.98\89.56\79.69 | 98.68\99.08\89.29\79.52 | 99.01\98.98\89.02\79.06 | 99.01\99.18\88.55\78.49 | 99.34\98.67\87.43\77.05 | 98.68\98.57\98.57\75.98 | 98.35\98.47\85.77\74.80 | 96.70\96.32\82.21\61.19 | 97.36\96.93\82.37\63.05 | 97.03\96.63\82.33\63.29 | 99.01\97.24\82.25\64.42 | 98.68\97.85\82.37\65.40 | 98.02\97.96\82.95\66.47 | 98.35\98.26\83.14\66.62 |
*euk/met/ver/act
Euk: Dataset with 303 genes of Eukaryota library profile.
Met: Dataset with 978 genes of Metazoa library profile.
Ver: Dataset with 2586 genes of Vertebrata library profile
Actino: Dataset with 4584 genes of Actinopterygii library profile.