BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714083.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 = 431,778 number of mapped reads = 321,331 (74.42%) number of supplementary alignments = 11,909 (2.76%) number of secondary alignments = 0 number of mapped bases = 41,231,735 bp number of sequenced bases = 40,390,939 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 261,750 duplication rate = 42.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.3907 >>>>>>> ACTG content number of A's = 11,200,199 bp (27.73%) number of C's = 8,655,191 bp (21.43%) number of T's = 10,600,490 bp (26.24%) number of G's = 9,934,748 bp (24.6%) number of N's = 311 bp (0%) GC percentage = 46.03% >>>>>>> Mismatches and indels general error rate = 0.0434 number of mismatches = 1,618,626 number of insertions = 44,272 mapped reads with insertion percentage = 13.35% number of deletions = 139,491 mapped reads with deletion percentage = 41.47% homopolymer indels = 28.39% >>>>>>> Coverage mean coverageData = 0.0133X std coverageData = 1.687X 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 0.03% 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 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% 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 3787634 0.015196086512458478 1.7608045065227995 chr2 243199373 4211419 0.017316734611811685 3.537382277777832 chr3 198022430 2040221 0.010302979314010034 0.9475943084716856 chr4 191154276 2004350 0.010485509620511969 1.1865492456855316 chr5 180915260 2312066 0.01277982852303338 1.2250191680795357 chr6 171115067 1624918 0.009496054488293541 0.900880820645258 chr7 159138663 1609712 0.010115153474677615 1.0864195756526762 chr8 146364022 1951077 0.01333030462909799 1.5115411213127339 chr9 141213431 1687650 0.01195105867798085 1.5669831000682977 chr10 135534747 2167226 0.015990187372393886 1.555856007132994 chr11 135006516 1850375 0.013705819947238695 1.4370661088884784 chr12 133851895 1799392 0.013443156706896081 1.434279976939555 chr13 115169878 1031180 0.00895355641515918 0.9775438451208964 chr14 107349540 1239807 0.01154925302893706 1.245164630997366 chr15 102531392 1189358 0.011599940045678889 1.1048796727534802 chr16 90354753 1467601 0.01624265410807996 1.8161729212913444 chr17 81195210 1628675 0.020058757160674873 2.159607239925452 chr18 78077248 967526 0.012391907050822283 1.137894230108992 chr19 59128983 804253 0.01360167145103781 1.3871895057931205 chr20 63025520 1038628 0.016479483231554456 1.5543763341628205 chr21 48129895 292275 0.006072629080117462 0.5885706275278054 chr22 51304566 541645 0.010557442392164471 1.1841891745782769 chrMT 16571 250889 15.140245006336372 140.28306663261858 chrX 155270560 3569437 0.022988498270373983 1.806710692007847 chrY 59373566 164421 0.002769262671539722 0.49219531265011696