BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173987.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 8,114,578 number of mapped reads = 7,956,914 (98.06%) number of supplementary alignments = 1,066,222 (13.14%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,978,366 number of mapped paired reads (second in pair) = 3,978,548 number of mapped paired reads (both in pair) = 7,853,518 number of mapped paired reads (singletons) = 103,396 number of mapped bases = 898,432,578 bp number of sequenced bases = 897,815,922 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,519,940 duplication rate = 65.59% >>>>>>> Insert size mean insert size = 1,018,596.974 std insert size = 9,763,511.0727 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 52.7211 >>>>>>> ACTG content number of A's = 266,718,948 bp (29.71%) number of C's = 179,936,060 bp (20.04%) number of T's = 264,658,537 bp (29.48%) number of G's = 186,495,338 bp (20.77%) number of N's = 7,039 bp (0%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 7,081,121 number of insertions = 89,952 mapped reads with insertion percentage = 1.09% number of deletions = 260,338 mapped reads with deletion percentage = 3.2% homopolymer indels = 41.31% >>>>>>> Coverage mean coverageData = 0.2902X std coverageData = 4.6958X There is a 5.86% of reference with a coverageData >= 1X There is a 4.44% of reference with a coverageData >= 2X There is a 3.36% of reference with a coverageData >= 3X There is a 2.74% of reference with a coverageData >= 4X There is a 2.1% of reference with a coverageData >= 5X There is a 1.76% of reference with a coverageData >= 6X There is a 1.35% of reference with a coverageData >= 7X There is a 1.19% of reference with a coverageData >= 8X There is a 0.91% of reference with a coverageData >= 9X There is a 0.83% of reference with a coverageData >= 10X There is a 0.63% of reference with a coverageData >= 11X There is a 0.58% of reference with a coverageData >= 12X There is a 0.44% of reference with a coverageData >= 13X There is a 0.41% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.15% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.07% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 78442258 0.3147123874166797 2.123479280168754 chr2 243199373 82189563 0.33795137703747286 15.459062170697393 chr3 198022430 63009257 0.318192524957905 1.7787968375350542 chr4 191154276 58208740 0.30451183838545154 1.9832627727145307 chr5 180915260 52852822 0.29214131522128095 1.6896623389207117 chr6 171115067 52903498 0.309169139383851 1.8616536758045688 chr7 159138663 48151561 0.30257613135784606 1.9065276960544064 chr8 146364022 45766506 0.31268958979550315 2.3625359518204525 chr9 141213431 38485445 0.27253388525061756 1.849577656209692 chr10 135534747 44879675 0.3311304000884733 2.344528096247072 chr11 135006516 42554883 0.31520614160578736 1.8047134950388979 chr12 133851895 40978055 0.306144750509509 1.7988676591363482 chr13 115169878 27045768 0.23483369497013795 1.5323833648850191 chr14 107349540 28471432 0.2652217419841762 1.6402365334913163 chr15 102531392 28943490 0.2822890573844935 1.7152201446887194 chr16 90354753 26264392 0.2906808012634377 1.8751800392883826 chr17 81195210 27532628 0.339091776473021 1.8856361465454707 chr18 78077248 21930179 0.28087797100635514 2.277863513101603 chr19 59128983 17541511 0.29666519040247996 1.7500235263207633 chr20 63025520 20828619 0.33047912972395943 1.8364626861630424 chr21 48129895 11533361 0.23962988076329692 1.73242443181859 chr22 51304566 11987824 0.2336599826222095 1.6206787088309471 chrMT 16571 1304866 78.74395027457606 67.97773505345178 chrX 155270560 22039877 0.14194498300257305 1.179430590168777 chrY 59373566 4586368 0.07724595824343783 1.1938857379793573