Figure Legend
Figure 1. Comparison of two mapping strategies. A: Comparison of CRT. B: Comparison of LRE. C: Comparison of MT. “Bwa mem” were performed using default parameter values. And, “Bwa aln” was used with MS parameters.
Figure 2. Comparison of BWA mem results with “-k” parameters. A: Comparison of CRT B: Comparison of LRE. C: Comparison of MT.
Figure 3. Comparison of “BWA mem” results with “-r” parameters. A: Comparison of CRT B: Comparison of LRE. C: Comparison of MT.
Figure 4. Comparison of deamination filtering with “-DetectRange” parameters. A: Comparison of the CRT after filtering. B: Comparison of the LRE after filtering.
Figure 5. The homologous contamination rate after filtering by use of the AncFil with the parameters –DeamNum=15 –DetectRange=1 –DoubleOrSingle=or. X axis means the rate of homologous contamination which was added in simulation data. Y axis means the rate of homologous contamination which was remaining after filtering.
Figure S1. Species information of the top 10 simulated exogenous contaminations
Figure S2. the damage pattern distribution of 6 samples
Figure S3. Comparison of deamination filtering with “-DeamNum” parameters. A: Comparison of the CRT after filtering. B: Comparison of the LRE after filtering.
Figure S4. Comparison of deamination filtering with “-DoubleOrSingle” parameters. A: Comparison of the CRT after filtering. B: Comparison of the LRE after filtering.
Data availability: Raw sequencing data of the ancient panda have been deposited to the CNSA (CNGB Nucleotide Sequence Archive) with accession number CNP0000732 (https://db.cngb.org/cnsa/).
Conflicts of Interest: The authors declare no conflicts of interest.
Author Contributions: conceptualization, T.M.L., X.Y.Z., Y.C.X., K.L.Z. and K.K.; methodology, T.M.L. and W.H.X.; software, W.H.X. and T.M.L.; validation, H.M.L., Y.L., Y.M., X.S.G. and J.N.N.; data curation, T.M.L. and Y.P.T.; investigation, T.M.L., W.H.X., H.B.G; writing–original draft preparation, T.M.L. and W.H.X., and J.N.N.; writing—review and editing, T.M.L. and J.N.N.; visualization, W.H.X and T.M.L.; supervision, T.M.L. and X.Y.Z..