BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714075.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 347,218 number of mapped reads = 335,552 (96.64%) number of supplementary alignments = 14,810 (4.27%) number of secondary alignments = 0 number of mapped bases = 43,566,664 bp number of sequenced bases = 42,772,229 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 278,297 duplication rate = 42.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.1495 >>>>>>> ACTG content number of A's = 12,765,245 bp (29.84%) number of C's = 8,603,691 bp (20.12%) number of T's = 11,966,483 bp (27.98%) number of G's = 9,436,546 bp (22.06%) number of N's = 264 bp (0%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0386 number of mismatches = 1,519,069 number of insertions = 45,874 mapped reads with insertion percentage = 13.23% number of deletions = 131,245 mapped reads with deletion percentage = 37.38% homopolymer indels = 27.08% >>>>>>> Coverage mean coverageData = 0.0141X std coverageData = 2.1059X There is a 0.05% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2844622 0.011412697744091076 2.125881749518337 chr2 243199373 4014303 0.01650622265378949 2.362964732909457 chr3 198022430 2596627 0.013112792323576677 1.4812911669426212 chr4 191154276 3495451 0.018286020449785806 3.7109429130232012 chr5 180915260 2251347 0.012444207304569 1.559751787161212 chr6 171115067 2741290 0.016020155606753204 2.3300162435389957 chr7 159138663 1846914 0.011605690064142363 1.6900844516393312 chr8 146364022 2058153 0.014061877856841076 1.5886531881697448 chr9 141213431 1737502 0.012304084588101255 1.7355395248608603 chr10 135534747 1939665 0.014311200949819901 2.00204622481209 chr11 135006516 1908411 0.014135695494875224 2.172580545756439 chr12 133851895 1734166 0.012955856919321164 2.1344532884839666 chr13 115169878 1354880 0.011764187160118377 1.2776371711841368 chr14 107349540 1207007 0.011243709102060429 1.4831009836895777 chr15 102531392 1496401 0.014594564365223873 2.0306668632939435 chr16 90354753 664853 0.0073582515354781615 0.9482880174257006 chr17 81195210 507107 0.006245528523172734 0.9801833719110515 chr18 78077248 940782 0.012049374486149922 1.5262900939982396 chr19 59128983 249297 0.0042161557218056665 0.49630520595983013 chr20 63025520 616550 0.009782545229297593 1.2451607300399237 chr21 48129895 491027 0.010202120740134588 2.0364691545882736 chr22 51304566 196258 0.0038253515291407007 0.6113067697813953 chrMT 16571 2236 0.1349345241687285 0.7339852094014316 chrX 155270560 6446766 0.041519564301178535 3.786808332355219 chrY 59373566 225049 0.0037903904912836126 0.6167809984028688