Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing

BMC Genomics

Table 5 Summary of the 59,955 contigs that aligned with regions of the zebra finch genome assembly, but had no match in the zebra finch cDNA database

a) classes A and B	total	distance to nearest gene (bp)
		< 2,500	< 5,000	< 7,500	< 10,000
	19,357	5,843	8,429	9,778	10,752
	19,721	5,708	8,227	9,621	10,570
b) classes C ¹and D ²	total	alignment position of contig
		start position
	84	penultimate intron	final intron	final exon	3' UTR
		1	7	74	2
		end position
	97	first exon		first intron
		86		11
c) class E ³	total	gene length (bp)		length of alignment with genome sequence (bp)
	49	64-202		131-1,235
d) class F ⁴	total	aligns to one gene feature ⁵		aligns to more than one gene feature ⁶
		20,387		260
		one gene feature ⁵, contig aligns to
		5'UTR	3'UTR	exons	introns
	20,647	4	89	4	20,290
		more than one gene feature ⁶, contig aligns to
		contig start		contig end
		exons	introns	exons	introns	3' UTR
		111	149	105	152	3

Contigs are shown in grey while genes are in black
¹ class C contigs align to genes with a mean of 10.5 exons (range 1-35 exons), 18% of genes have only one exon
² class D contigs align to genes with a mean of 8.4 exons (range 1-33 exons), 20% of genes have only one exon
³ 48 contigs extend from 5' (upstream) to 3' (downstream) of the closest mapped gene and one contig extends from the start position (i.e., the start of the 5'UTR) of the closest gene to 3' of the gene. All genes have only one exon
⁴ class F contigs align to genes with a mean of 16.4 exons (range 1-149 exons), 87% of genes have more than five exons
⁵ for example, the start and end of the contig are both within the 5' UTR
⁶ for example, the start of the contig aligns within exon 1 and the end of the contig aligns within intron 1

ISSN: 1471-2164