BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013219.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 = 1,009,324 number of mapped reads = 884,820 (87.66%) number of supplementary alignments = 5,395 (0.53%) number of secondary alignments = 0 number of mapped bases = 60,261,011 bp number of sequenced bases = 60,235,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,984 duplication rate = 1.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2114 >>>>>>> ACTG content number of A's = 17,365,940 bp (28.83%) number of C's = 10,997,649 bp (18.26%) number of T's = 19,007,641 bp (31.56%) number of G's = 12,863,459 bp (21.36%) number of N's = 897 bp (0%) GC percentage = 39.61% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 466,274 number of insertions = 4,926 mapped reads with insertion percentage = 0.55% number of deletions = 14,497 mapped reads with deletion percentage = 1.62% homopolymer indels = 46.94% >>>>>>> Coverage mean coverageData = 0.0195X std coverageData = 0.2926X There is a 1.79% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4318830 0.017327258735295187 0.6413777479394737 chr2 243199373 5629085 0.02314596839030502 0.3054870972535852 chr3 198022430 3744676 0.018910362831119687 0.14417779080894252 chr4 191154276 4038792 0.021128441824654762 0.16073028821638266 chr5 180915260 3388828 0.018731576319211546 0.14694855042025903 chr6 171115067 3307906 0.01933147126079786 0.1794833333176478 chr7 159138663 3331930 0.02093727531190833 0.3801255359486074 chr8 146364022 3632328 0.024817082438469747 0.37335758632108357 chr9 141213431 2629447 0.01862037471492354 0.2674266590786505 chr10 135534747 2990057 0.022061184059317274 0.2273136792343875 chr11 135006516 2709006 0.020065742604601394 0.21519214410341458 chr12 133851895 2587817 0.019333435660361775 0.1525318947453649 chr13 115169878 1767630 0.015348023551783219 0.1290453005431794 chr14 107349540 1998794 0.018619492920044185 0.15822919428975935 chr15 102531392 1572551 0.01533726373284779 0.13185248939829294 chr16 90354753 1838727 0.020350086065754613 0.17815997448960755 chr17 81195210 1322317 0.016285652811292687 0.15405499068414313 chr18 78077248 1996613 0.025572276830248934 0.5319993510708206 chr19 59128983 1090762 0.01844716321266679 0.396646162771423 chr20 63025520 1321208 0.02096306385096069 0.16050311597083328 chr21 48129895 1034692 0.02149790686225266 0.16435823730924104 chr22 51304566 587420 0.011449663174228976 0.11125734045894978 chrMT 16571 4427 0.26715346086536723 0.5268891645358915 chrX 155270560 3269478 0.02105665104833782 0.17893735026125518 chrY 59373566 147690 0.0024874706026584287 0.07304744007561348