BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231787.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 = 10,560,220 number of mapped reads = 5,875,834 (55.64%) number of supplementary alignments = 39,110 (0.37%) number of secondary alignments = 0 number of mapped bases = 398,188,971 bp number of sequenced bases = 398,034,742 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 300,140 duplication rate = 2.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0959 >>>>>>> ACTG content number of A's = 112,754,233 bp (28.33%) number of C's = 84,123,950 bp (21.13%) number of T's = 106,160,771 bp (26.67%) number of G's = 94,964,182 bp (23.86%) number of N's = 31,606 bp (0.01%) GC percentage = 44.99% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 2,402,526 number of insertions = 31,087 mapped reads with insertion percentage = 0.52% number of deletions = 89,831 mapped reads with deletion percentage = 1.51% homopolymer indels = 43.8% >>>>>>> Coverage mean coverageData = 0.1286X std coverageData = 11.2901X There is a 9.77% of reference with a coverageData >= 1X There is a 1.92% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 42324550 0.16980719979831063 3.403253320082041 chr2 243199373 36414239 0.14972998717393898 40.02429195286045 chr3 198022430 36188574 0.18274987333505605 0.5326315870751949 chr4 191154276 9366384 0.04899908176785959 0.31118397455373104 chr5 180915260 17094677 0.09448996729186913 0.3911846976846014 chr6 171115067 29494688 0.17236756831004252 0.8845857067984422 chr7 159138663 28659245 0.18008976863152357 2.2765641949106765 chr8 146364022 16972936 0.11596385346666682 0.7818861715833416 chr9 141213431 13045877 0.09238410898748009 0.7034230077451283 chr10 135534747 17001172 0.1254377373796256 1.0580712753779704 chr11 135006516 13371665 0.09904458981816848 0.7886584849604764 chr12 133851895 15997098 0.11951342190560695 0.42552828210349436 chr13 115169878 12399701 0.10766444503831114 0.3868166901941167 chr14 107349540 15577580 0.14511082208642906 0.5549428430126512 chr15 102531392 7626488 0.07438198049627572 0.3271777500734966 chr16 90354753 12943571 0.1432527960095248 0.579064668239834 chr17 81195210 12231538 0.15064359092118856 0.5703678562970876 chr18 78077248 8239862 0.10553473913424817 1.720307790535457 chr19 59128983 14962403 0.2530468518289922 1.8521182683251134 chr20 63025520 13130218 0.20833176782992033 0.6041880211414493 chr21 48129895 8182359 0.17000575214219768 0.538631668328164 chr22 51304566 4331437 0.08442595538182703 0.35119448663548536 chrMT 16571 196634 11.866151710820107 7.3999670591098035 chrX 155270560 11679053 0.07521743336277012 0.43124455290591224 chrY 59373566 757022 0.012750152146832481 0.20739947621579152