BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525184.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 = 2,645,042 number of mapped reads = 2,446,212 (92.48%) number of supplementary alignments = 7,122 (0.27%) number of secondary alignments = 0 number of mapped bases = 143,212,961 bp number of sequenced bases = 143,169,161 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,915 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8303 >>>>>>> ACTG content number of A's = 37,048,492 bp (25.88%) number of C's = 25,063,185 bp (17.51%) number of T's = 45,155,320 bp (31.54%) number of G's = 35,898,592 bp (25.07%) number of N's = 3,572 bp (0%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 713,957 number of insertions = 9,612 mapped reads with insertion percentage = 0.39% number of deletions = 27,799 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.92% >>>>>>> Coverage mean coverageData = 0.0463X std coverageData = 0.4299X There is a 4.02% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.06% 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 14472270 0.05806312514663705 0.7874132537606691 chr2 243199373 11375750 0.046775408421797206 0.5228337696115606 chr3 198022430 10060317 0.050803926605688055 0.26128471367372463 chr4 191154276 7876482 0.04120484335908865 0.24029408095569973 chr5 180915260 6243315 0.034509609637130664 0.21071308930521748 chr6 171115067 8537402 0.049892754330043886 0.2901599596295543 chr7 159138663 10357322 0.06508363087102222 0.7619366178647565 chr8 146364022 9777277 0.06680109542220697 0.39945660313543896 chr9 141213431 4498509 0.03185609873043875 0.29129806123716034 chr10 135534747 7967669 0.05878691019359043 0.48616846202691505 chr11 135006516 6218666 0.04606196933487269 0.334811896243772 chr12 133851895 6084146 0.045454313515695836 0.24207275687992452 chr13 115169878 4343464 0.03771354173006938 0.2206147224005051 chr14 107349540 5145084 0.04792832833750382 0.2561208630838047 chr15 102531392 3713704 0.036220165624982446 0.21715324272007 chr16 90354753 4098339 0.04535831114495991 0.2767964510266691 chr17 81195210 2402528 0.02958952874190485 0.2085936851648607 chr18 78077248 2978039 0.038142212696840955 0.6431929060068515 chr19 59128983 2558497 0.043269761632801974 0.5245478041165353 chr20 63025520 2429241 0.03854376766744646 0.22335161264314493 chr21 48129895 1432190 0.02975676551964221 0.20457769836967463 chr22 51304566 1425549 0.02778600641510153 0.1852925722766738 chrMT 16571 542879 32.76078691690302 18.44335252752842 chrX 155270560 8293386 0.053412482057126606 0.2903913278917914 chrY 59373566 380936 0.0064159191651045515 0.13694917857899044