Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery

Table 6 Subset of those contigs constructed from all five cDNA libraries combined (20,741 individual reads).

Contig ID	Length	Depth	# SNPs	bp per SNP	Ts/Tv ratio	Top BLAST hit	GENBANK ID	Bit score	e-value
Contig18.1	421	28	5	84.2	0.7	CXXC finger 6	XP_001072947.1	53	7.00E-06
Contig19.1	379	27	8	47.4	0.5	Ribosomal S20	XP_001514106.1	181	2.00E-44
Contig26.1	630	24	2	315.0	0.0	ORF2	AAC60281.1	89	1.00E-22
Contig61.1	465	13	1	465.0	0.0	Calmodulin Complex	2VAY	202	7.00E-51
Contig65.1	553	13	7	79.0	0.8	Endonuclease-reverse transcriptase	XP_001182458.1	80	6.00E-14
Contig176.1	311	7	14	22.2	0.4	Polyprotein	AAN12398.1	89	1.00E-16
Contig278.1	485	5	3	161.7	0.0	Tc1-like transporase	BAF37936.1	121	2.00E-26

The contigs listed below include only those with a significant BLAST hit and at least one SNP and with a Ts/Tv ratio < 1.0 (see Methods). In other words, the SNPs described in this table are a subset of the 877 we identified, but includes all of those associated with a particular gene and with a Ts/Tv ratio < 1.0. See additional file 5 for information from those contigs that produced a Ts/Tv ratio ≥ 1.0.

ISSN: 1471-2164