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Table 1 Alignment of Kmar RNA-Seq reads against various reference genomes

From: Transcriptomics of diapause in an isogenic self-fertilizing vertebrate

Reference Genome/Transcriptome No. of Mapped RNA-Seq Reads: Percentage:
RNA01:pre-Dia RNA02:Dia-R1 RNA03:Dia-R2 RNA04:Dia-R3 RNA05:post-Dia RNA01:pre-Dia RNA02:Dia-R1 RNA03:Dia-R2 RNA04:Dia-R3 RNA05:post-Dia
Kmar de novo Genome (ABySS)a 31,590,161 39,192,211 31,524,390 32,811,042 30,944,064 97.08 97.42 97.35 97.32 96.98
Kmar de novo Transcriptome (Trans-ABySS)a 30,584,171 37,850,616 30,651,957 31,942,287 29,994,937 93.99 94.08 94.66 94.74 94.01
Kmar de novo Transcriptome (Trinity)a 29,039,228 35,715,712 29,057,499 30,264,954 28,112,433 89.24 88.78 89.74 89.77 88.11
Kmar de novo Partial-Genome (ABySS, RADSeq)b 4,078,090 4,631,901 3,720,990 3,781,213 3,789,332 12.53 11.51 11.49 11.22 11.88
Amazon Molly Genomec 3,735,199 4,105,696 3,022,398 3,096,027 2,577,109 11.48 10.21 9.33 9.18 8.08
Platyfish Genomed 3,250,075 3,733,889 2,736,897 2,824,479 2,278,491 9.99 9.28 8.45 8.38 7.14
Medaka Genomee 3,668,978 3,476,396 2,512,691 2,499,786 2,198,448 11.28 8.64 7.76 7.41 6.89
Zebrafish Genomef 1,841,434 1,552,206 1,124,437 1,073,152 982,792 5.66 3.86 3.47 3.18 3.08
Fugu Genomeg 1,302,617 1,557,208 1,097,370 1,143,775 1,036,617 4.00 3.87 3.39 3.39 3.25
Mouse Genomeh 1,324,000 998,352 763,984 712,118 639,505 4.07 2.48 2.36 2.11 2.00
Human Genomei 1,681,163 1,273,803 961,456 899,559 853,593 5.17 3.17 2.97 2.67 2.68
  1. aThis study;
  2. b(Mesak, et al. [32]);
  3. cPoeFor_5.1.2;
  4. dXipmac4.4.2 (Schartl, et al. [40]);
  5. eoryLat2, MEDAKA1 (Kasahara, et al. [41]);
  6. fdanRer7, Zv9 (Howe, et al. [42]);
  7. gfr3, FUGU4 (Aparicio, et al. [43]);
  8. hmm10, GRCm38 (Mouse Genome Sequencing, et al. [44]);
  9. ihg38, GRCh38 (Lander, et al. [45]; Venter, et al. [46]);
  10. Reference genome database can be downloaded from http://www.ensembl.org/info/data/ftp/index.html or http://hgdownload.soe.ucsc.edu/downloads.html
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