BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524617.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 = 4,047,276 number of mapped reads = 3,761,746 (92.95%) number of supplementary alignments = 7,996 (0.2%) number of secondary alignments = 0 number of mapped bases = 219,008,464 bp number of sequenced bases = 218,937,440 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 293,861 duplication rate = 5.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2802 >>>>>>> ACTG content number of A's = 55,718,863 bp (25.45%) number of C's = 42,316,765 bp (19.33%) number of T's = 68,727,717 bp (31.39%) number of G's = 52,172,664 bp (23.83%) number of N's = 1,431 bp (0%) GC percentage = 43.16% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 1,023,255 number of insertions = 16,150 mapped reads with insertion percentage = 0.43% number of deletions = 41,650 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.85% >>>>>>> Coverage mean coverageData = 0.0707X std coverageData = 0.5341X There is a 5.57% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 23924603 0.09598613196634724 1.0323521995821392 chr2 243199373 19223343 0.07904355493548086 0.6280939947397552 chr3 198022430 13924028 0.07031540820905996 0.3302869991385314 chr4 191154276 9555878 0.049990396238899726 0.34569998958268566 chr5 180915260 13190862 0.07291182623290042 0.3358787839132669 chr6 171115067 14103873 0.082423326287217 0.3912998828827327 chr7 159138663 12894328 0.0810257404261339 0.7138513503302497 chr8 146364022 19515786 0.13333731700813742 0.6833395408253427 chr9 141213431 8102837 0.05738007314615846 0.4663689407106529 chr10 135534747 9448435 0.06971227090570362 0.5282269283510984 chr11 135006516 11139127 0.0825080694623658 0.4916435521383843 chr12 133851895 6680807 0.049911934380906596 0.29007772503648277 chr13 115169878 4984820 0.0432823242202271 0.26191763568425247 chr14 107349540 3917447 0.03649244328387434 0.2598441879522549 chr15 102531392 5873800 0.05728782069007705 0.3231519951990461 chr16 90354753 6587387 0.07290581603382834 0.3657287913935083 chr17 81195210 5466035 0.06731967316791225 0.3352228555953582 chr18 78077248 5647871 0.07233696300361406 0.7862490311397835 chr19 59128983 4374712 0.07398591651745473 0.6863495306422542 chr20 63025520 3962370 0.06286929485072079 0.32362304423950594 chr21 48129895 2016535 0.04189776437284976 0.300288566465684 chr22 51304566 4960351 0.09668439647262585 0.3905182859113635 chrMT 16571 14214 0.8577635628507634 1.1463028716952106 chrX 155270560 8989525 0.05789587543189127 0.37600220022003594 chrY 59373566 509490 0.008581091457434105 0.22884690891300816