BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818876.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,581,806 number of mapped reads = 2,416,093 (93.58%) number of supplementary alignments = 37,414 (1.45%) number of secondary alignments = 0 number of mapped bases = 223,517,025 bp number of sequenced bases = 223,374,224 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 745,799 duplication rate = 26.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3507 >>>>>>> ACTG content number of A's = 64,853,080 bp (29.03%) number of C's = 46,941,437 bp (21.01%) number of T's = 64,427,391 bp (28.84%) number of G's = 47,149,103 bp (21.11%) number of N's = 3,213 bp (0%) GC percentage = 42.12% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,343,894 number of insertions = 34,440 mapped reads with insertion percentage = 1.37% number of deletions = 73,183 mapped reads with deletion percentage = 2.96% homopolymer indels = 39.68% >>>>>>> Coverage mean coverageData = 0.0722X std coverageData = 0.856X There is a 4.3% of reference with a coverageData >= 1X There is a 1.54% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 20949116 0.08404840042504849 1.2789834675391918 chr2 243199373 16754246 0.06889099175432496 1.3562202006307862 chr3 198022430 13774333 0.06955945849164663 0.39968833819736393 chr4 191154276 11250740 0.058856857588684024 0.5251120638814789 chr5 180915260 11259342 0.06223544658421849 0.4099425562441696 chr6 171115067 11028308 0.06444966064852722 0.42982576792101584 chr7 159138663 19724014 0.12394231312600634 1.7402976775704877 chr8 146364022 20012090 0.13672820496829474 0.7132863270967099 chr9 141213431 8123330 0.05752519390312101 0.6610672309620428 chr10 135534747 10203981 0.07528682663199275 1.1213638894509859 chr11 135006516 9639535 0.07140051669802368 0.49310586972918685 chr12 133851895 8784484 0.0656283872559294 0.3950856789139643 chr13 115169878 6807735 0.059110377802084675 0.36622566754478897 chr14 107349540 6632847 0.06178738166926472 0.42135380163161407 chr15 102531392 6082447 0.05932277794492442 0.37621570269239996 chr16 90354753 5578161 0.06173622100433388 0.9667943109542307 chr17 81195210 5559338 0.06846879267877995 0.5081766480466225 chr18 78077248 4164370 0.053336536656619866 0.757308388928301 chr19 59128983 3801875 0.06429799409876541 1.1133687778640695 chr20 63025520 9159608 0.14533173228876176 0.6384065649928252 chr21 48129895 2146855 0.04460543701580899 0.41284895623872075 chr22 51304566 1988092 0.03875078097337379 0.3481328972533881 chrMT 16571 239936 14.479271015629715 9.391687991678198 chrX 155270560 9019371 0.05808809474249336 0.45047839122590017 chrY 59373566 832871 0.014027639842282676 1.1144906751312023