Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates

BMC Genomics

Table 5 BAC sequence assemblies generated using standard versus copy-control bacterial host cells.

BAC sequence [GenBank:]	Species	ENCODE Region	Redundancy variation		No. contigs >2 kb		No. uncaptured gaps
			Standard	Copy control	Standard	Copy control	Standard	Copy control
AC190087	Cat	ENm011	++++	-	18	13	6	2
AC153092	Platypus	ENm009	++++	-	15	8	13	3
AC188899	Owl Monkey	ENm006	++++	-	14	9	6	3
AC190076	Owl Monkey	ENm011	++	-	22	15	9	1
AC182792	Shrew	ENr331	++	-	22	11	11	0
AC175233	Shrew	ENr322	++	+	21	22	9	10
AC186717	Platypus	ENm006	++	-	20	10	7	3
AC188506	Rabbit	ENm006	++	+	11	6	5	0
AC190002	Owl Monkey	ENr312	++	++	10	6	5	4
AC187194	Platypus	ENr312	++	+	9	12	7	3
AC172296	Hedgehog	ENr211	+	-	21	13	9	0
AC190000	Owl Monkey	ENm007	+	-	10	6	2	0
AC188356	Dusky Titi	ENm006	+	-	8	13	0	2

Representative BACs whose generated sequences were associated with atypical characteristics (in terms of large numbers of contigs and uncaptured gaps) were tested. Two exceptions [GenBank: AC190000 and AC188356] represent typical sequence assemblies with respect to redundancy of sequence reads, number of contigs, and number of uncaptured gaps. Only three BACs [GenBank: AC190002, AC187194, and AC172296] belong to the second data set (Tables 2 and 3), while the remaining BACs have sequences orthologous to other ENCODE regions. The variation in the redundancy of sequence reads across all contigs was qualitatively assessed as low (-), medium (+), high (++), or very high (++++); see Figure 4 for illustrative examples.

ISSN: 1471-2164