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Table 1 Silver fox transcriptome: summary statistics of reads and assemblies.

From: Sequence comparison of prefrontal cortical brain transcriptome from a tame and an aggressive silver fox (Vulpes vulpes)

Run Total number of reads Number of filtered bases (Gb) Average (median) read length in bp +/- S.D. Fully aligned (%)* Partially aligned (%)* Number of Isogroups* Number of Isotigs* Average Isotig Length N50 Isotig Length Number of Contigs* (length >= 100 bp) Total number of bases in contigs at least 100 bp in length Singletons* (%) Repeats* (%)* Outliers* (%)* Too Short* (%)*
Tame 2,565,892 0.96 376 +/-148 (433) 1,921,335 (74.9%) 250,138 (9.7%) 37,679 50,311 1,565 2,473 55,656 52,072,035 287,577 (11.2%) 1,321 (0.1%) 78,309 (3.1%) 26,993 (1.1%)
Aggressive 3,379,343 1.21 358 +/-146 (403) 2,458,444 (72.7%) 338,660 (10.0%) 44,791 60,492 1,593 2,647 67,078 60,587,572 426,108 (12.6%) 1,023 (0.1%) 118,205 (3.6%) 36,637 (1.1%)
All Together 5,945,235 2.17   4,551,142 (76.6%) 571,726 (9.6%) 59,713 87,400 1,820 3,293 96,461 83,773,326 562,591 (9.5%) 14,192 (0.2%) 181,469 (3.1%) 63,630 1.1%
  1. The number of reads is tabulated for both samples (Tame, Aggressive), both individually and all together, with the total number of bases for each set that passed filtering criteria and were used for mapping against the canine RefSeq database, together with analytic results of the corresponding fox transcriptome assemblies. Isogroups: an isogroup is a collection of contigs containing reads with implied connections between them, analogous to individual genes; Isotigs: an isotig is meant to be analogous to an individual transcript or splice variant; Contigs: a contig represents the consensus sequence of a self-consistent set of overlapping reads, roughly analogous to exons; Singletons: reads that did not overlap with any other reads in the input; Repeats: reads that were either inferred to be repetitive early in the assembly process or determined to partially overlap a contig; Outliers: reads that were identified by the GS De Novo Assembler as problematic, and were excluded from the final contigs; Too Short: the trimmed read was too short (< 50bp) to used in the computation. (see also Methods).