BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234030.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 = 1,179,282 number of mapped reads = 898,353 (76.18%) number of supplementary alignments = 3,479 (0.3%) number of secondary alignments = 0 number of mapped bases = 59,790,093 bp number of sequenced bases = 59,761,233 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,943 duplication rate = 2.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2317 >>>>>>> ACTG content number of A's = 16,683,354 bp (27.92%) number of C's = 10,439,650 bp (17.47%) number of T's = 19,526,116 bp (32.67%) number of G's = 13,101,017 bp (21.92%) number of N's = 11,096 bp (0.02%) GC percentage = 39.39% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 464,357 number of insertions = 4,886 mapped reads with insertion percentage = 0.54% number of deletions = 16,377 mapped reads with deletion percentage = 1.8% homopolymer indels = 47.27% >>>>>>> Coverage mean coverageData = 0.0193X std coverageData = 0.1898X There is a 1.69% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% 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 3985437 0.0159896773135823 0.22918555722243558 chr2 243199373 6590310 0.027098384007758113 0.21818720063599814 chr3 198022430 4224838 0.021335148750573355 0.1626110289068076 chr4 191154276 3038511 0.015895595241615205 0.14551429261942417 chr5 180915260 1598156 0.008833726906176958 0.10443851108643068 chr6 171115067 4806189 0.02808746818303265 0.2030036851218951 chr7 159138663 4578361 0.028769633435967727 0.29243217224256446 chr8 146364022 2905613 0.019851961980110112 0.22786563938692436 chr9 141213431 1991366 0.014101817269775139 0.14940771034806935 chr10 135534747 3824752 0.02821971549480223 0.2058681178376118 chr11 135006516 3875124 0.028703236812658732 0.21698796067754114 chr12 133851895 1739602 0.012996468970424363 0.1286318214576852 chr13 115169878 2876808 0.024978823021762686 0.17783738357114745 chr14 107349540 1562667 0.014556811328674533 0.14921981132680137 chr15 102531392 1411909 0.013770504549474955 0.13086293168864574 chr16 90354753 1908910 0.021126835463763594 0.17322231304023164 chr17 81195210 1212970 0.014938935437201283 0.1456123317481509 chr18 78077248 382647 0.004900877141571384 0.3054414539066732 chr19 59128983 1386386 0.023446809494423404 0.19636006843185794 chr20 63025520 1143254 0.018139540935164043 0.15432649091408263 chr21 48129895 966088 0.02007251418271326 0.16282874456392155 chr22 51304566 425491 0.00829343337589095 0.09971998953732147 chrMT 16571 23704 1.430450787520367 1.6732602174523017 chrX 155270560 3180944 0.0204864592489394 0.16478924074077078 chrY 59373566 150056 0.0025273199861365913 0.07610464730796797