Table 2 Overview of RNA-seq read alignments
From: Transcriptome analysis of egg viability in rainbow trout, Oncorhynchus mykiss
Egg quality group | Female ID# | rRNA removal | Poly(A) retention | ||||||
|---|---|---|---|---|---|---|---|---|---|
Total reads | Mapped to transcriptome (%) | Mapped to mitochondrial RNA (%) | Mapped to rRNA (%) | Total reads | Mapped to transcriptome (%) | Mapped to mitochondrial RNA (%) | Mapped to rRNA (%) | ||
Low quality | 48 | 37,157,250 | 43.6 | 3.1 | 8.3 | 61,999,239 | 30.3 | 32.7 | 2.4 |
63 | 39,461,498 | 48.5 | 2.4 | 5.4 | 64,750,933 | 39.3 | 22.3 | 2.0 | |
129 | 58,281,853 | 54.8 | 2.4 | 3.7 | 59,599,504 | 39.1 | 18.4 | 3.3 | |
136 | 36,865,244 | 47.3 | 1.6 | 5.7 | 43,578,497 | 34.8 | 20.8 | 3.0 | |
Mean | 42,941,461 | 48.6 | 2.4 | 5.8 | 57,482,043 | 35.9 | 23.6 | 2.7 | |
Medium quality | 13 | 37,890,847 | 44.9 | 3.0 | 7.6 | 64,816,319 | 20.9 | 53.9 | 5.7 |
60 | 36,566,538 | 49.0 | 2.9 | 4.4 | 60,757,076 | 13.8 | 62.5 | 4.2 | |
71 | 33,120,194 | 51.2 | 5.0 | 4.1 | 55,561,085 | 12.9 | 61.2 | 12.7 | |
106 | 37,362,260 | 49.0 | 2.7 | 5.1 | 62,699,350 | 24.7 | 45.5 | 3.0 | |
108 | 53,796,039 | 52.9 | 6.8 | 5.5 | 61,835,604 | 24.5 | 45.6 | 2.6 | |
114 | 32,683,461 | 41.3 | 6.5 | 7.7 | 59,163,406 | 11.7 | 64.7 | 2.4 | |
Mean | 38,569,890 | 48.1 | 4.5 | 5.7 | 60,805,473 | 18.1 | 55.6 | 5.1 | |
High quality | 19 | 37,448,462 | 46.1 | 3.3 | 7.7 | 66,890,967 | 32.3 | 35.5 | 2.8 |
47 | 37,299,964 | 48.1 | 3.0 | 4.6 | 61,202,732 | 34.6 | 27.9 | 2.2 | |
58 | 36,637,099 | 43.5 | 2.1 | 6.2 | 61,065,293 | 37.6 | 26.6 | 1.8 | |
59 | 31,040,335 | 50.2 | 4.9 | 5.2 | 52,972,699 | 10.5 | 64.2 | 15.0 | |
87 | 38,856,780 | 49.7 | 2.8 | 5.0 | 55,700,910 | 18.8 | 53.3 | 5.9 | |
97 | 38,254,940 | 51.0 | 2.5 | 4.1 | 61,667,813 | 20.8 | 48.1 | 7.4 | |
99 | 55,069,888 | 52.7 | 4.8 | 3.2 | 68,472,008 | 25.4 | 46.3 | 1.7 | |
102 | 32,044,365 | 49.0 | 5.8 | 5.4 | 57,053,445 | 10.6 | 65.2 | 9.1 | |
103 | 39,749,239 | 48.1 | 1.7 | 4.1 | 59,550,700 | 23.8 | 43.2 | 4.3 | |
119 | 51,515,745 | 51.4 | 8.1 | 5.6 | 62,330,132 | 15.9 | 61.7 | 2.7 | |
Mean | 39,791,682 | 49.0 | 3.9 | 5.1 | 60,690,670 | 23.0 | 47.2 | 5.3 | |
All | Mean | 40,055,100 | 48.6 | 3.8 | 5.4 | 60,083,386 | 24.1 | 45.0 | 4.7 |