BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013195.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 = 2,237,176 number of mapped reads = 1,951,097 (87.21%) number of supplementary alignments = 13,897 (0.62%) number of secondary alignments = 0 number of mapped bases = 129,481,933 bp number of sequenced bases = 129,428,925 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,519 duplication rate = 3.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5674 >>>>>>> ACTG content number of A's = 35,870,343 bp (27.71%) number of C's = 23,638,226 bp (18.26%) number of T's = 41,307,220 bp (31.91%) number of G's = 28,611,261 bp (22.11%) number of N's = 1,875 bp (0%) GC percentage = 40.37% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 902,905 number of insertions = 8,830 mapped reads with insertion percentage = 0.45% number of deletions = 30,398 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.49% >>>>>>> Coverage mean coverageData = 0.0418X std coverageData = 0.3758X There is a 3.44% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11324579 0.04543450666066746 0.7364816194183554 chr2 243199373 12873722 0.052934848643709294 0.43048363353147756 chr3 198022430 8898121 0.04493491469627961 0.25012787986918567 chr4 191154276 8665206 0.045330955609907464 0.25589095384041766 chr5 180915260 6362791 0.03517000721774382 0.2211788547125561 chr6 171115067 7822694 0.0457159859569818 0.3214778353065332 chr7 159138663 8912820 0.056006628634299886 0.5032095742511882 chr8 146364022 6516054 0.04451950630326352 0.427745896456608 chr9 141213431 4471856 0.03166735606048691 0.30497457845242215 chr10 135534747 5603587 0.04134428346997984 0.3320846109428539 chr11 135006516 6601844 0.048900187899078885 0.36697081392686065 chr12 133851895 5095788 0.03807034633316174 0.23308021025445783 chr13 115169878 3571657 0.031012075917975706 0.20727614220292842 chr14 107349540 4178212 0.03892156407936168 0.23888252246941127 chr15 102531392 2908321 0.02836517619891477 0.20273193527237138 chr16 90354753 4666928 0.05165116216963152 0.27745683175530483 chr17 81195210 3064640 0.03774409845112784 0.25409257061573765 chr18 78077248 3609356 0.04622801254470445 0.5498331319354062 chr19 59128983 2326696 0.03934950141117766 0.4832070990015295 chr20 63025520 2060323 0.03269029751757701 0.21903819458645377 chr21 48129895 1998725 0.041527724089154984 0.2481679931307584 chr22 51304566 1163501 0.022678312881547424 0.17328907221144335 chrMT 16571 20617 1.2441614869350068 1.3191017860327938 chrX 155270560 6487296 0.04178059253473421 0.27121420861268836 chrY 59373566 276599 0.00465862198676091 0.1068164829930401