Table 4.
Number of transcripts assembled (TA) with Cufflinks and the percentage they represent in each sample
| Code |
L1 |
L2 |
L3 |
L4 |
L5 |
H1 |
H2 |
H3 |
H4 |
H5 |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| TA | % | TA | % | TA | % | TA | % | TA | % | TA | % | TA | % | TA | % | TA | % | TA | % | |
| = |
1971 |
8.7 |
2486 |
10.4 |
2526 |
11 |
2244 |
9.2 |
2762 |
10.2 |
2642 |
10.1 |
2363 |
9.4 |
2761 |
9.9 |
2119 |
10.4 |
2838 |
10.5 |
| c |
4059 |
17.8 |
4202 |
17.6 |
3953 |
17.2 |
4203 |
17.3 |
4289 |
15.9 |
3955 |
15.1 |
4083 |
16.3 |
4183 |
15.0 |
3569 |
17.5 |
3961 |
14.7 |
| e |
745 |
3.3 |
508 |
2.1 |
518 |
2.3 |
672 |
2.8 |
576 |
2.1 |
616 |
2.4 |
736 |
2.9 |
604 |
2.2 |
489 |
2.4 |
529 |
2.0 |
| i |
3115 |
13.7 |
2719 |
11.4 |
2629 |
11.4 |
3153 |
13.0 |
3248 |
12.0 |
3301 |
12.6 |
3373 |
13.5 |
3637 |
13.1 |
2250 |
11.0 |
3234 |
12.0 |
| j |
4348 |
19.1 |
4709 |
19.7 |
4436 |
19.3 |
4666 |
19.2 |
5373 |
19.9 |
5288 |
20.2 |
4833 |
19.3 |
5658 |
20.3 |
3488 |
17.1 |
5428 |
20.1 |
| o |
1067 |
4.7 |
1175 |
4.9 |
1139 |
5.0 |
1157 |
4.8 |
1237 |
4.6 |
1142 |
4.4 |
1154 |
4.6 |
1170 |
4.2 |
1129 |
5.5 |
1204 |
4.5 |
| p |
1570 |
6.9 |
1656 |
6.9 |
1566 |
6.8 |
1682 |
6.9 |
1635 |
6.1 |
1603 |
6.1 |
1606 |
6.4 |
1676 |
6.0 |
1699 |
8.3 |
1598 |
5.9 |
| s |
60 |
0.3 |
77 |
0.3 |
72 |
0.3 |
76 |
0.3 |
94 |
0.4 |
86 |
0.3 |
71 |
0.3 |
72 |
0.3 |
68 |
0.3 |
100 |
0.4 |
| u |
4447 |
19.5 |
4560 |
19.1 |
4541 |
19.7 |
4789 |
19.7 |
5468 |
20.2 |
5456 |
20.9 |
5089 |
20.3 |
5680 |
20.4 |
4421 |
21.7 |
5638 |
20.9 |
| x |
1392 |
6.1 |
1838 |
7.7 |
1630 |
7.1 |
1663 |
6.8 |
2346 |
8.7 |
2066 |
7.9 |
1761 |
7.0 |
2415 |
8.7 |
1192 |
5.8 |
2496 |
9.2 |
| Total | 22774 | 100 | 23930 | 100 | 23010 | 100 | 24305 | 100 | 27028 | 100 | 26155 | 100 | 25069 | 100 | 27856 | 100 | 20424 | 100 | 27026 | 100 |
Class codes described by Cuffcompare: "=" Exactly equal to the reference annotation, "c " Contained in the reference annotation, "e" possible pre-mRNA molecule, "i " An exon falling into an intron of the reference, "j " New isoforms, "o" Unknown, generic overlap with reference, "p" Possible polymerase run-on fragment, “s” An intron of the transfrag overlapping a reference intron on the opposite strand, "u" Unknown, intergenic transcript, “x” Exonic overlap with reference on the opposite strand. L1 to L5 and H1 to H5 correspond to animals of the L and H groups, respectively.