Table 1

Statistics of the number of fragments sequenced, aligned and mapped using TopHat

Sample

Sequenced fragmentsa

All mapped fragments (%)

Uniquely mapped fragments (%)b

Singleton fragments (%)c

Spliced fragments (%)d

Multi-loci mapped fragments (%)


Control

1295-ZZ-4

10,114,082

84.5

45.2

24.9

3.8

26.1

1295-ZZ-9

6,152,569

82.0

46.1

24.5

3.3

26.2

1295-ZZ-13

9,263,358

86.5

50.6

25.0

3.2

21.2

Case

1295-ZZ-21

9,287,780

85.8

50.7

25.1

3.3

20.9

1295-ZZ-32

8,911,007

85.4

48.5

26.3

4.0

21.2

1295-ZZ-36

8,211,577

86.6

50.7

23.3

3.2

22.8


aEach fragment has two short sequence reads.

bFor uniquely mapped fragments, both of the two reads could be uniquely mapped to a unique location in the reference genome.

cFor singleton fragments, only one of the two reads could be mapped to the reference genome.

dFor spliced fragments, at least one of the two reads could be mapped across a splicing junction.

Xu et al. BMC Genomics 2012 13(Suppl 8):S2   doi:10.1186/1471-2164-13-S8-S2

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