BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173896.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 6,229,730 number of mapped reads = 6,056,153 (97.21%) number of supplementary alignments = 606,642 (9.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,035,096 number of mapped paired reads (second in pair) = 3,021,057 number of mapped paired reads (both in pair) = 5,942,444 number of mapped paired reads (singletons) = 113,709 number of mapped bases = 717,002,957 bp number of sequenced bases = 716,624,372 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,854,222 duplication rate = 66.04% >>>>>>> Insert size mean insert size = 737,948.3976 std insert size = 7,996,174.3683 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.7686 >>>>>>> ACTG content number of A's = 216,050,036 bp (30.15%) number of C's = 140,027,813 bp (19.54%) number of T's = 215,531,765 bp (30.08%) number of G's = 145,006,125 bp (20.23%) number of N's = 8,633 bp (0%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 7,385,243 number of insertions = 72,058 mapped reads with insertion percentage = 1.15% number of deletions = 156,525 mapped reads with deletion percentage = 2.52% homopolymer indels = 43.17% >>>>>>> Coverage mean coverageData = 0.2316X std coverageData = 3.2829X There is a 4.38% of reference with a coverageData >= 1X There is a 3.54% of reference with a coverageData >= 2X There is a 2.82% of reference with a coverageData >= 3X There is a 2.38% of reference with a coverageData >= 4X There is a 1.88% of reference with a coverageData >= 5X There is a 1.56% of reference with a coverageData >= 6X There is a 1.2% of reference with a coverageData >= 7X There is a 0.98% of reference with a coverageData >= 8X There is a 0.75% of reference with a coverageData >= 9X There is a 0.62% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 56197118 0.22546430486125046 2.2737932554379485 chr2 243199373 64181909 0.26390655620645864 9.895510952961365 chr3 198022430 59693187 0.3014465937015317 1.691367941064794 chr4 191154276 36704003 0.19201246118083176 1.4915928995343373 chr5 180915260 48280081 0.26686571934285697 1.5554109739494386 chr6 171115067 39189721 0.22902554221014332 1.7494363942611355 chr7 159138663 29624943 0.18615804884574153 1.81565557969442 chr8 146364022 45817563 0.3130384255223596 2.221130987275782 chr9 141213431 24353757 0.17246062805456516 1.7328445863564843 chr10 135534747 30043674 0.22166768791769687 2.856771072023406 chr11 135006516 25674262 0.19017053962047284 1.375570059379051 chr12 133851895 33758457 0.2522075387875532 1.5254248593160513 chr13 115169878 19824039 0.17212867934096449 1.269533599384452 chr14 107349540 22849942 0.21285551852388002 1.3987616921406842 chr15 102531392 25128771 0.2450836812983091 1.4877942545593152 chr16 90354753 24275460 0.2686683234029758 2.0183468574864447 chr17 81195210 29550056 0.36393841459366877 1.9919007315390276 chr18 78077248 14698964 0.1882618096375528 2.6401352920228534 chr19 59128983 11542504 0.19520890457392104 1.8476174021904157 chr20 63025520 31092136 0.4933261320176335 2.3250135170569792 chr21 48129895 9352084 0.19430925415482414 1.3815651656262622 chr22 51304566 5486376 0.10693738253238513 0.9409334993879841 chrMT 16571 1159281 69.95842133848289 53.98944993539691 chrX 155270560 27312592 0.17590322337988606 1.2670854504601534 chrY 59373566 1212077 0.020414421461564226 0.764782203686687