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

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

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%

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).

ISSN: 1471-2164