BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524608.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 = 1,812,997 number of mapped reads = 1,692,148 (93.33%) number of supplementary alignments = 3,470 (0.19%) number of secondary alignments = 0 number of mapped bases = 98,807,038 bp number of sequenced bases = 98,775,432 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,646 duplication rate = 3.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5029 >>>>>>> ACTG content number of A's = 24,603,392 bp (24.91%) number of C's = 17,378,666 bp (17.59%) number of T's = 31,115,803 bp (31.5%) number of G's = 25,676,973 bp (26%) number of N's = 598 bp (0%) GC percentage = 43.59% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 454,866 number of insertions = 6,296 mapped reads with insertion percentage = 0.37% number of deletions = 18,614 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.04% >>>>>>> Coverage mean coverageData = 0.0319X std coverageData = 0.2868X There is a 2.8% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 10144808 0.040701234601939064 0.5105690453906071 chr2 243199373 8775294 0.03608271638101633 0.3308187210948662 chr3 198022430 6382457 0.03223098009654765 0.20126857561659883 chr4 191154276 4493261 0.02350594030133022 0.19527288345004523 chr5 180915260 6169753 0.034102999382141674 0.20661201564514478 chr6 171115067 6458367 0.037742830676623 0.23569176252065258 chr7 159138663 6005077 0.03773487150636674 0.38830950056762187 chr8 146364022 8853689 0.06049088347681509 0.38060945344371605 chr9 141213431 3619486 0.025631315480182618 0.25067356855744577 chr10 135534747 4240972 0.031290662312595016 0.28261763508587645 chr11 135006516 5036745 0.037307421517343654 0.28031555293909277 chr12 133851895 3029323 0.022631902222975626 0.17323902435224015 chr13 115169878 2424069 0.021047769105043246 0.16633283249299616 chr14 107349540 1820022 0.016954166734203052 0.15300418105505928 chr15 102531392 2497826 0.02436157308778174 0.17880879579308886 chr16 90354753 2860758 0.031661400258600675 0.21174475497679648 chr17 81195210 2138363 0.026336073273287918 0.1897635244937412 chr18 78077248 2689785 0.03445030490828775 0.4109873538985445 chr19 59128983 1922895 0.03252034624035391 0.35257273050812477 chr20 63025520 1832505 0.029075603025568057 0.19498702918157362 chr21 48129895 886486 0.01841861487543241 0.16717347026256987 chr22 51304566 1766569 0.03443297814857259 0.2064786367845408 chrMT 16571 6961 0.420071208738157 0.7520705214946661 chrX 155270560 4514584 0.029075595528218614 0.2204340496521997 chrY 59373566 236983 0.003991389029926213 0.11429536258309812