BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068119.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 = 2,851,811 number of mapped reads = 709,938 (24.89%) number of supplementary alignments = 5,767 (0.2%) number of secondary alignments = 0 number of mapped bases = 44,299,686 bp number of sequenced bases = 44,283,180 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,041 duplication rate = 10.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9381 >>>>>>> ACTG content number of A's = 11,595,558 bp (26.19%) number of C's = 7,868,642 bp (17.77%) number of T's = 14,308,112 bp (32.31%) number of G's = 10,467,802 bp (23.64%) number of N's = 43,066 bp (0.1%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 433,752 number of insertions = 3,268 mapped reads with insertion percentage = 0.46% number of deletions = 10,307 mapped reads with deletion percentage = 1.44% homopolymer indels = 46.69% >>>>>>> Coverage mean coverageData = 0.0143X std coverageData = 0.2643X There is a 0.82% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 3745858 0.01502848010958416 0.30443317304138495 chr2 243199373 3733627 0.015352124283642786 0.28286787071450215 chr3 198022430 2836412 0.014323690503141487 0.2117522830243948 chr4 191154276 3050742 0.015959580208396697 0.45289850600041504 chr5 180915260 2703419 0.014943012546315883 0.21992307809229458 chr6 171115067 2689290 0.015716266528417396 0.24289785682805518 chr7 159138663 2341102 0.014711082497909386 0.231493681347701 chr8 146364022 2249012 0.01536588001114099 0.23311396886295033 chr9 141213431 1789285 0.0126707848349071 0.21206548562497823 chr10 135534747 2135644 0.01575716963562119 0.2501448276879572 chr11 135006516 2012435 0.014906206453027792 0.22434095215069505 chr12 133851895 2048800 0.015306469885988539 0.22081482230270308 chr13 115169878 1409369 0.012237305660773558 0.20125181726546904 chr14 107349540 1293012 0.012044876950567277 0.21609695122431158 chr15 102531392 1268510 0.012371918251144 0.42461397218657954 chr16 90354753 1298333 0.014369282820130115 0.21623550512931983 chr17 81195210 1161289 0.014302432372550055 0.20956928167467467 chr18 78077248 1170563 0.014992370120422278 0.28440778506587144 chr19 59128983 841019 0.014223464658609129 0.2555319505549571 chr20 63025520 910671 0.014449242148259944 0.205646757939152 chr21 48129895 541491 0.011250616690520517 0.178929285068979 chr22 51304566 540503 0.01053518316478888 0.17298206375257397 chrMT 16571 12187 0.7354414338301852 2.461288911971883 chrX 155270560 2374119 0.015290206978064613 0.2283295134873125 chrY 59373566 142994 0.0024083781661354145 0.1881049533155565