BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525238.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 = 373,647 number of mapped reads = 345,512 (92.47%) number of supplementary alignments = 1,166 (0.31%) number of secondary alignments = 0 number of mapped bases = 20,372,279 bp number of sequenced bases = 20,365,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,071 duplication rate = 1.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6303 >>>>>>> ACTG content number of A's = 5,360,911 bp (26.32%) number of C's = 3,577,953 bp (17.57%) number of T's = 6,463,525 bp (31.74%) number of G's = 4,962,364 bp (24.37%) number of N's = 462 bp (0%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 100,125 number of insertions = 1,690 mapped reads with insertion percentage = 0.49% number of deletions = 4,375 mapped reads with deletion percentage = 1.25% homopolymer indels = 40.53% >>>>>>> Coverage mean coverageData = 0.0066X std coverageData = 0.0943X There is a 0.63% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 2098620 0.008419718240140312 0.1403256008390195 chr2 243199373 1662204 0.0068347380155457885 0.09971378151092045 chr3 198022430 2107542 0.010642945852144124 0.1055759323593107 chr4 191154276 936699 0.004900225198205872 0.07298314756626445 chr5 180915260 885639 0.00489532502675562 0.07154061431814074 chr6 171115067 1235713 0.007221532397261078 0.08931535934046829 chr7 159138663 1142964 0.007182189283568381 0.11668915331490236 chr8 146364022 1292243 0.008828966178587248 0.10890394131609672 chr9 141213431 691532 0.004897069599562382 0.07583643451060126 chr10 135534747 1062875 0.007842084952576774 0.10665550355615976 chr11 135006516 905421 0.006706498521893566 0.08804365995276311 chr12 133851895 835392 0.006241166776159575 0.08113805630633403 chr13 115169878 626520 0.005439964085053559 0.07526004066672783 chr14 107349540 739797 0.006891478063157048 0.08541216298564165 chr15 102531392 527596 0.005145702108482054 0.07370564490588175 chr16 90354753 502444 0.005560792136745701 0.07804062524620346 chr17 81195210 377144 0.004644904545477498 0.06977699007619433 chr18 78077248 438726 0.005619127354488724 0.10365151350695706 chr19 59128983 356048 0.0060215478422823545 0.10212900742838248 chr20 63025520 351883 0.005583182812295718 0.07655938889622789 chr21 48129895 241183 0.0050110851062525694 0.07269269775181372 chr22 51304566 161311 0.003144184086851061 0.05741798455330608 chrMT 16571 528 0.0318628930058536 0.17563498812921965 chrX 155270560 1129746 0.007275983290071215 0.08862794354794742 chrY 59373566 62509 0.001052808584884391 0.04187334934156578