BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716735.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 = 1,458,651 number of mapped reads = 1,345,845 (92.27%) number of supplementary alignments = 7,462 (0.51%) number of secondary alignments = 0 number of mapped bases = 78,831,405 bp number of sequenced bases = 78,808,862 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,094 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1087 >>>>>>> ACTG content number of A's = 20,040,528 bp (25.43%) number of C's = 16,629,398 bp (21.1%) number of T's = 23,388,354 bp (29.68%) number of G's = 18,749,617 bp (23.79%) number of N's = 965 bp (0%) GC percentage = 44.89% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 382,189 number of insertions = 5,777 mapped reads with insertion percentage = 0.43% number of deletions = 14,366 mapped reads with deletion percentage = 1.06% homopolymer indels = 40.55% >>>>>>> Coverage mean coverageData = 0.0255X std coverageData = 0.2429X There is a 2.33% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 6772127 0.027169950360926082 0.34402980882063017 chr2 243199373 7007016 0.028811817701520144 0.2876257591563034 chr3 198022430 5873706 0.029661821643134065 0.1956007233239034 chr4 191154276 4100685 0.021452227414468093 0.16655990282921537 chr5 180915260 3894424 0.021526232778815893 0.15622664561395969 chr6 171115067 4244987 0.024807792057259342 0.17841654865364065 chr7 159138663 4842116 0.030427024512578695 0.49881440927815235 chr8 146364022 5977535 0.04084019363720409 0.2571985230332694 chr9 141213431 3275467 0.02319515202488069 0.17919771514964283 chr10 135534747 3457927 0.025513213965714637 0.2960387271546244 chr11 135006516 2771835 0.020531120142378907 0.18228280558668708 chr12 133851895 3649347 0.027264066750791984 0.18831335885797718 chr13 115169878 1929319 0.016751940989292356 0.13772570487671218 chr14 107349540 2570396 0.02394417339841419 0.16751349205543573 chr15 102531392 1895974 0.018491644003038602 0.14735650726997407 chr16 90354753 2629761 0.029104844102667185 0.18785154893625552 chr17 81195210 3925268 0.04834359071181662 0.2457562867009649 chr18 78077248 1747845 0.02238609895676651 0.2673450501898362 chr19 59128983 1772086 0.029969837296203793 0.30434847438967677 chr20 63025520 1696418 0.026916366576586755 0.18150257897658212 chr21 48129895 783432 0.016277450844220623 0.14152603331227898 chr22 51304566 1485076 0.02894627351491483 0.1827882669039437 chrMT 16571 32576 1.9658439442399371 1.8711044558328422 chrX 155270560 2339877 0.015069675796879975 0.14729216318568872 chrY 59373566 156205 0.0026308845926485197 0.07435576885618787