BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716396.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 = 1,989,213 number of mapped reads = 1,827,070 (91.85%) number of supplementary alignments = 27,747 (1.39%) number of secondary alignments = 0 number of mapped bases = 144,015,376 bp number of sequenced bases = 143,950,479 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,336 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3169 >>>>>>> ACTG content number of A's = 35,866,931 bp (24.92%) number of C's = 27,183,691 bp (18.88%) number of T's = 45,651,059 bp (31.71%) number of G's = 35,240,777 bp (24.48%) number of N's = 8,021 bp (0.01%) GC percentage = 43.37% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,214,302 number of insertions = 13,198 mapped reads with insertion percentage = 0.71% number of deletions = 37,010 mapped reads with deletion percentage = 1.99% homopolymer indels = 43.99% >>>>>>> Coverage mean coverageData = 0.0465X std coverageData = 0.5002X There is a 3.95% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11761906 0.04718907400435323 0.7858222565635862 chr2 243199373 12378471 0.05089844947914401 0.7668481810061462 chr3 198022430 9379015 0.0473633971666745 0.251532312039006 chr4 191154276 9275443 0.04852333515155057 0.2863983851830616 chr5 180915260 8642742 0.0477723216935929 0.25553482489755003 chr6 171115067 8335626 0.04871357120176916 0.3094910704730964 chr7 159138663 7808924 0.04906993594636396 0.610454425003803 chr8 146364022 7369691 0.050351793420926896 0.6806029196620106 chr9 141213431 6121575 0.043349807144052746 0.5643549509600916 chr10 135534747 6931058 0.05113860580711454 0.48051615725368213 chr11 135006516 6404383 0.0474375844199994 0.48314974532740884 chr12 133851895 6456183 0.04823378107571805 0.25775840149551127 chr13 115169878 4629312 0.04019551014892974 0.227504807941787 chr14 107349540 4358384 0.040599931774276815 0.31298565498791864 chr15 102531392 4129870 0.04027907862598803 0.23724117823701243 chr16 90354753 4208807 0.046580914232591614 0.29794368693869555 chr17 81195210 3854558 0.047472726531528155 0.27457547426703177 chr18 78077248 4050582 0.051879159470374775 1.0551603937079344 chr19 59128983 2960925 0.050075696380571945 0.5742434785532308 chr20 63025520 2970871 0.04713758807543357 0.26468795334155215 chr21 48129895 1930645 0.040113218613919685 0.2609381350136757 chr22 51304566 1662407 0.032402710511185304 0.20590920571117557 chrMT 16571 11530 0.6957938567376742 1.0419797758819933 chrX 155270560 7986950 0.05143892055261474 0.37868897880897834 chrY 59373566 395518 0.006661516675619585 0.1923891730121903