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Table 1 Outcome of sequencing experiments

From: Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone

Library

Pre-treatment

Mapped reads (excluding duplicates)

Endogenous contenta (%)

Relative DNA quantityb (%)

Mean fragment length

GC content (total/mapped), %

(GP1-01)

None

(4896)

(0.7)

(0.4)

(37.7)

(60/37)

GP1-02

None

2969

0.4

100.0

31.9

64/37

GP1-03

None

3409

0.4

39.0

34.1

63/38

GP1-07

0.1% bleach

28,771

3.5

4.7

36.5

60/37

GP1-10

0.1% bleach

16,898

2.6

2.4

32.8

62/39

GP1-08

0.5% bleach

33,467

3.8

1.3

40.1

57/38

GP1-11

0.5% bleach

23,317

3.1

0.7

36.1

59/39

GP1-09

1.0% bleach

18,865

2.1

1.1

39.6

57/38

GP1-12

1.0% bleach

16,590

2.1

0.7

37.8

59/39

GP1-13

Pre-digestion

5734

0.7

11.7

36.6

62/39

GP1-14

Pre-digestion

4925

0.7

11.3

34.3

62/39

  1. The number of mapped reads, endogenous contents, relative DNA quantities and GC contents of all libraries are reported. GP1-01 (shown in parentheses) is considered an outlier due to an extremely reduced relative DNA quantity in comparison to other untreated libraries (GP1-02 and GP1-03), suggesting failed library preparation, and was not considered for further analysis
  2. aEndogenous content was calculated as the quotient of successfully mapped reads (excluding duplicates) and the total number of reads used for mapping
  3. bBased on qPCR results (Additional file 2: Table S1). Normalised to GP1-02 (untreated), which yielded the most DNA