BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525093.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 = 3,026,323 number of mapped reads = 2,719,838 (89.87%) number of supplementary alignments = 70,102 (2.32%) number of secondary alignments = 0 number of mapped bases = 208,072,522 bp number of sequenced bases = 207,992,355 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,351 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4052 >>>>>>> ACTG content number of A's = 56,557,968 bp (27.19%) number of C's = 39,420,187 bp (18.95%) number of T's = 63,212,366 bp (30.39%) number of G's = 48,794,391 bp (23.46%) number of N's = 7,443 bp (0%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,486,740 number of insertions = 20,402 mapped reads with insertion percentage = 0.74% number of deletions = 47,212 mapped reads with deletion percentage = 1.71% homopolymer indels = 40.56% >>>>>>> Coverage mean coverageData = 0.0672X std coverageData = 0.6507X There is a 5.63% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 16345773 0.06557966810441768 0.975888764302492 chr2 243199373 17811606 0.07323870033168219 1.007561948365569 chr3 198022430 14295401 0.0721908169695726 0.3063444995749683 chr4 191154276 13807590 0.072232702762035 0.3364249546836703 chr5 180915260 12865715 0.07111459254459795 0.3242444570436931 chr6 171115067 12215740 0.07138903788057424 0.3779383802985047 chr7 159138663 11639037 0.07313770758523967 1.005262504010483 chr8 146364022 10668372 0.07288930608916992 0.9710268453328669 chr9 141213431 8844609 0.06263291626984122 0.6790905446389043 chr10 135534747 9861894 0.07276284656361959 0.5945705351407303 chr11 135006516 9507835 0.07042500822701031 0.6563698692536177 chr12 133851895 9309573 0.06955129772350253 0.3120795153249619 chr13 115169878 6829022 0.05929520911709223 0.2758005280052969 chr14 107349540 6455479 0.06013513425395209 0.37202624573414045 chr15 102531392 6025991 0.05877215633627601 0.28350420150406863 chr16 90354753 5782386 0.06399647841436742 0.34263079468509516 chr17 81195210 5096701 0.0627709565625854 0.4155951663621534 chr18 78077248 5785370 0.07409802661077398 1.2107801190395786 chr19 59128983 3694874 0.06248837393330442 0.7809620394109517 chr20 63025520 4152465 0.06588545401926077 0.31035262673222275 chr21 48129895 2680685 0.055696880286150635 0.3086303014837987 chr22 51304566 2009799 0.03917388171649284 0.22520139807633033 chrMT 16571 4841 0.2921368656085933 0.6759203727853716 chrX 155270560 11911531 0.07671467791447394 0.49157627091285433 chrY 59373566 470233 0.007919904962420482 0.16962781490839868