BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231864.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,270,516 number of mapped reads = 925,457 (72.84%) number of supplementary alignments = 5,399 (0.42%) number of secondary alignments = 0 number of mapped bases = 58,693,285 bp number of sequenced bases = 58,661,437 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,906 duplication rate = 5.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2478 >>>>>>> ACTG content number of A's = 15,839,982 bp (27%) number of C's = 9,831,017 bp (16.76%) number of T's = 19,630,853 bp (33.46%) number of G's = 13,356,967 bp (22.77%) number of N's = 2,618 bp (0%) GC percentage = 39.53% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 446,812 number of insertions = 4,822 mapped reads with insertion percentage = 0.52% number of deletions = 18,062 mapped reads with deletion percentage = 1.93% homopolymer indels = 46.62% >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 0.194X There is a 1.58% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% 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 5626781 0.022574792301119282 0.24696623601742726 chr2 243199373 4354838 0.017906452415072632 0.2103540487069706 chr3 198022430 4752076 0.023997665314984772 0.18098446582436803 chr4 191154276 2823513 0.014770859742630083 0.15052181549300298 chr5 180915260 2892515 0.015988231175192186 0.14726142999372424 chr6 171115067 3863459 0.022578134513426572 0.19826169478822125 chr7 159138663 4029508 0.025320735539923443 0.25494709115065767 chr8 146364022 3673640 0.025099337595409887 0.32591914578902353 chr9 141213431 2361219 0.016720923663415557 0.16718795378653606 chr10 135534747 2133516 0.015741468864807043 0.16995449457747847 chr11 135006516 2361573 0.017492289038849057 0.1701619299968375 chr12 133851895 2330731 0.017412760573916417 0.15524581974616142 chr13 115169878 2464632 0.021399970572166447 0.17236485660140266 chr14 107349540 2204710 0.020537675336102977 0.17015815458884892 chr15 102531392 1458547 0.014225370118841263 0.14392871085302972 chr16 90354753 1188267 0.013151128862031198 0.13713080323426305 chr17 81195210 1342632 0.016535852299661518 0.15573650758446694 chr18 78077248 1346387 0.01724429375379624 0.25002475040805044 chr19 59128983 1135401 0.019202106012883732 0.17881617964039687 chr20 63025520 1487247 0.023597536363047858 0.1820682599141395 chr21 48129895 1449383 0.030113986328039983 0.20746517227177974 chr22 51304566 551921 0.010757736455659717 0.11947881645138007 chrMT 16571 28641 1.7283809064027518 1.7326810194646503 chrX 155270560 2587148 0.016662192755664693 0.1532367388263089 chrY 59373566 245000 0.004126415448922168 0.08571027579140739