BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524361.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 = 2,261,535 number of mapped reads = 2,074,472 (91.73%) number of supplementary alignments = 10,019 (0.44%) number of secondary alignments = 0 number of mapped bases = 121,185,537 bp number of sequenced bases = 121,151,089 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,498 duplication rate = 4.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9761 >>>>>>> ACTG content number of A's = 28,580,247 bp (23.59%) number of C's = 25,090,490 bp (20.71%) number of T's = 38,639,807 bp (31.89%) number of G's = 28,823,739 bp (23.79%) number of N's = 16,806 bp (0.01%) GC percentage = 44.5% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 630,373 number of insertions = 8,967 mapped reads with insertion percentage = 0.43% number of deletions = 21,991 mapped reads with deletion percentage = 1.05% homopolymer indels = 42.18% >>>>>>> Coverage mean coverageData = 0.0391X std coverageData = 0.3804X There is a 3.29% of reference with a coverageData >= 1X There is a 0.44% 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 9786997 0.03926568752661202 0.7602930642244854 chr2 243199373 10181741 0.04186581928399955 0.5097349916186473 chr3 198022430 7935710 0.0400748036472434 0.2334238624437532 chr4 191154276 7666577 0.040106751260955316 0.27601178447929836 chr5 180915260 7295760 0.040326946438901834 0.2330587601096985 chr6 171115067 6941209 0.04056456933742719 0.25526672132598055 chr7 159138663 6717602 0.04221225611277129 0.45505147344458163 chr8 146364022 6308639 0.04310238891904733 0.33300337983741096 chr9 141213431 5147114 0.036449181664596764 0.31291340203161333 chr10 135534747 5960879 0.04398044879222005 0.3646718140727351 chr11 135006516 5370006 0.039775902372001064 0.3154324776378726 chr12 133851895 5346526 0.03994359586765656 0.2396797754223373 chr13 115169878 3717455 0.03227801456905251 0.20920212912389244 chr14 107349540 3596892 0.03350635689729085 0.23168402489707385 chr15 102531392 3559325 0.03471449017292187 0.2178501556787565 chr16 90354753 3691691 0.04085773993538558 0.2567421650387413 chr17 81195210 3355500 0.04132632947189865 0.25474115814993575 chr18 78077248 3034193 0.03886142349689374 0.5963530114099954 chr19 59128983 2588816 0.043782522016318125 0.4973995150789288 chr20 63025520 2729099 0.043301491205467245 0.24930439697573553 chr21 48129895 1622066 0.033701839573928014 0.24949272015481191 chr22 51304566 1542944 0.030074204311561666 0.20451074335325153 chrMT 16571 41140 2.4826504133727596 2.232294922043693 chrX 155270560 6642240 0.04277848936720522 0.2706141934292887 chrY 59373566 405416 0.00682822385975604 0.19465491760334078