Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus)

BMC Genomics

Table 1 BLAST statistics against three fish genome assemblies.

	# BACs one end	# BACs both ends	Sequences w/hit	BACs w/hit	Type 1*	Type 2*	Type 3*	Type 4*	3/(2+3)	(3+4)/(2+3+4)
Stickleback
Genoscope	6,734	30,649	11,229	10,048	7,987	797	54	153	0.063	0.206
Broad	12,758	56,118	21,754	19,510	14,405	1,416	142	633	0.054	0.286
Combined	19,492	86,767	33,053	29,558	22,392	2,213	196	786	0.057	0.259
Medaka
Genoscope	6,734	30,649	9,764	9,278	7,087	469	43	226	0.084	0.364
Broad	12,758	56,118	19,699	17,943	13,907	886	51	624	0.054	0.432
Combined	19,492	86,767	29,463	27,221	20,994	1,355	94	850	0.065	0.410
Tetraodon
Genoscope	6,734	30,649	6,931	6,386	3,879	265	14	62	0.050	0.222
Broad	12,758	56,118	14,260	13,227	7,279	503	19	188	0.036	0.291
Combined	19,492	86,767	21,191	19,613	11,158	768	33	250	0.041	0.269

*Numbers for type 1, 2, 3 & 4 do not include hits to the contigs in the 'unordered chromosome' of each genome assembly. Type 2 hits were scored when the two end sequences of a clone hit within 300 kb of each other in the target genome.

ISSN: 1471-2164