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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