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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