Table 3

Illumina sequencing and mapping results of liver and gill samples
Tissue (Specimen) No. read Retained reads Annotated transcriptome Reference transcriptome
% Mapped % Unmapped % Ambiguous % Mapped % Unmapped % Ambiguous
Liver (1) 47,999,274 31,104,129 68.5 28.0 3.4 75.8 19.8 4.4
Liver (2) 60,009,042 39,254,065 61.9 34.5 3.5 70.9 24.4 4.7
Liver (3) 47,666,040 26,435,958 62.4 33.9 3.6 71.2 24.0 4.8
Gill (1) 71,817,060 42,149,816 50.4 2.1 2.1 64.7 31.6 3.7
Gill (2) 50,157,764 29,490,860 52.9 2.8 44.0 69.7 25.9 4.4
Gill (3) 59,998,042 35,620,006 43.8 1.9 54.2 61.4 34.9 3.7

Results from Illumina sequencing of liver and gill samples from P. borchgrevinki held at their natural water temperatures. Sequenced 100 nt reads were processed using the Fastx toolkit and processed to remove the adaptor sequence used in library construction, low quality sections of each read, and any reads of uniformly low quality. Retained reads were thus shorter (80 nt) but of higher quality and used for read mapping with the program Bowtie.

Bilyk and Cheng

Bilyk and Cheng BMC Genomics 2013 14:634   doi:10.1186/1471-2164-14-634

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