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.

Blakesley et al. BMC Genomics 2010 11:21   doi:10.1186/1471-2164-11-21

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