BamQC report ----------------------------------- >>>>>>> Input bam file = SRR23117303.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP418207/SRP418207.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 = 635,255 number of mapped reads = 609,331 (95.92%) number of supplementary alignments = 4,736 (0.75%) number of secondary alignments = 0 number of mapped bases = 144,185,652 bp number of sequenced bases = 143,923,387 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,984 duplication rate = 22.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 53.4961 >>>>>>> ACTG content number of A's = 42,659,973 bp (29.64%) number of C's = 29,490,843 bp (20.49%) number of T's = 42,146,245 bp (29.28%) number of G's = 29,626,326 bp (20.58%) number of N's = 0 bp (0%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 732,473 number of insertions = 449,952 mapped reads with insertion percentage = 33.41% number of deletions = 208,189 mapped reads with deletion percentage = 23.77% homopolymer indels = 33.45% >>>>>>> Coverage mean coverageData = 0.0466X std coverageData = 0.8672X There is a 3.25% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 12152702 0.04875695776099992 2.679191117393104 chr2 243199373 12357227 0.05081109728025491 0.31830049927965515 chr3 198022430 10195062 0.051484379825053155 0.3069219807657661 chr4 191154276 9864202 0.051603355187304314 0.3571105647064035 chr5 180915260 9231955 0.05102916691494128 0.30542291747110556 chr6 171115067 8952960 0.052321283899564495 0.31045397636394867 chr7 159138663 7934288 0.04985770177043652 1.2154499118751867 chr8 146364022 7524745 0.05141116578499052 0.31346360771650594 chr9 141213431 5908811 0.04184312326495346 0.29009218158174616 chr10 135534747 6853884 0.05056920200692152 0.5114830553682571 chr11 135006516 6438641 0.04769133513526117 0.29623652683448937 chr12 133851895 6551738 0.04894766712118644 0.3002127011171417 chr13 115169878 4907491 0.04261088997593624 0.2766980628362646 chr14 107349540 4436837 0.04133074999669305 0.2769448108681986 chr15 102531392 3923428 0.03826562697988144 0.2626662164029968 chr16 90354753 3716092 0.04112779767103121 0.3536132249248763 chr17 81195210 3170753 0.039050985889438554 0.33291785159372705 chr18 78077248 3934604 0.0503937331397746 0.3449048413003501 chr19 59128983 1915877 0.032401656561554595 0.6797660630856025 chr20 63025520 2846850 0.0451697978850472 0.33006603878145724 chr21 48129895 1960416 0.04073177387983082 0.36516558760929885 chr22 51304566 1274340 0.024838724880744532 0.22108621990304453 chrMT 16571 60706 3.6633878462374025 6.984321977084989 chrX 155270560 7853093 0.05057683182182121 0.3079790341886538 chrY 59373566 218950 0.0036876680103735053 0.2699577299658411