BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716410.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 902,920 number of mapped reads = 760,118 (84.18%) number of supplementary alignments = 4,473 (0.5%) number of secondary alignments = 0 number of mapped bases = 44,303,385 bp number of sequenced bases = 44,289,948 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,499 duplication rate = 1.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0146 >>>>>>> ACTG content number of A's = 11,489,958 bp (25.94%) number of C's = 8,684,629 bp (19.61%) number of T's = 13,097,237 bp (29.57%) number of G's = 11,017,597 bp (24.88%) number of N's = 527 bp (0%) GC percentage = 44.48% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 222,642 number of insertions = 3,261 mapped reads with insertion percentage = 0.43% number of deletions = 8,419 mapped reads with deletion percentage = 1.1% homopolymer indels = 40.45% >>>>>>> Coverage mean coverageData = 0.0143X std coverageData = 0.1507X There is a 1.33% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3610724 0.014486318972902378 0.21207298000737196 chr2 243199373 3729403 0.01533475581781208 0.1773115222880676 chr3 198022430 2882110 0.014554462340453048 0.1269854271276686 chr4 191154276 2787030 0.014580003431364518 0.13771364968669583 chr5 180915260 2666899 0.014741150083193646 0.12811609248592315 chr6 171115067 2516360 0.014705660022328718 0.13299352756056032 chr7 159138663 2486193 0.015622809398618612 0.18389407307168804 chr8 146364022 2278257 0.015565690043691202 0.15669701221007537 chr9 141213431 1831467 0.012969495798172342 0.13069162810291685 chr10 135534747 2139369 0.015784653362727715 0.16165537341078243 chr11 135006516 2002699 0.014834091415261765 0.14277952320813553 chr12 133851895 1991904 0.014881403061196855 0.1294442384626425 chr13 115169878 1363281 0.011837131580533584 0.11455104580656252 chr14 107349540 1341670 0.01249814391379786 0.1197573383233066 chr15 102531392 1289494 0.012576577522716164 0.1197739790296199 chr16 90354753 1311760 0.01451788596002249 0.13140903256153852 chr17 81195210 1282688 0.015797582148010948 0.1385986308904918 chr18 78077248 1169314 0.014976373142659946 0.20819238563429762 chr19 59128983 924051 0.015627716783155225 0.17895175392644116 chr20 63025520 974045 0.015454771337071078 0.1330744664168514 chr21 48129895 572829 0.011901729683806707 0.12304985289329039 chr22 51304566 558933 0.010894410450718948 0.10947722818791572 chrMT 16571 6265 0.3780701225031682 0.7135164382923028 chrX 155270560 2449162 0.015773511733325363 0.13726917674988814 chrY 59373566 137478 0.0023154748697425385 0.07765930566705333