BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714268.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 = 351,782 number of mapped reads = 102,441 (29.12%) number of supplementary alignments = 3,763 (1.07%) number of secondary alignments = 0 number of mapped bases = 12,177,858 bp number of sequenced bases = 11,969,499 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,723 duplication rate = 40.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8656 >>>>>>> ACTG content number of A's = 2,784,336 bp (23.26%) number of C's = 2,097,021 bp (17.52%) number of T's = 2,605,935 bp (21.77%) number of G's = 4,481,988 bp (37.45%) number of N's = 219 bp (0%) GC percentage = 54.96% >>>>>>> Mismatches and indels general error rate = 0.0411 number of mismatches = 445,241 number of insertions = 13,380 mapped reads with insertion percentage = 11.91% number of deletions = 34,848 mapped reads with deletion percentage = 32.19% homopolymer indels = 31.3% >>>>>>> Coverage mean coverageData = 0.0039X std coverageData = 2.972X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 829109 0.003326406958079354 0.7679134527482607 chr2 243199373 3102057 0.012755201470030106 10.279505707723235 chr3 198022430 396499 0.0020022933765634528 0.4242495806688795 chr4 191154276 285787 0.0014950594147315856 0.3581478147120185 chr5 180915260 558994 0.003089811218799343 0.6449176132108094 chr6 171115067 352622 0.002060730280402485 0.3129028952629964 chr7 159138663 546591 0.0034346838769155675 1.1920960768582254 chr8 146364022 247041 0.00168785331684859 0.292680663188976 chr9 141213431 334333 0.0023675722460139077 0.42744328388730185 chr10 135534747 496262 0.0036615112433123886 0.588881565302309 chr11 135006516 554918 0.004110305312967265 1.0881254311834316 chr12 133851895 565551 0.004225199800122367 0.9648259326135056 chr13 115169878 293434 0.0025478363361642184 0.6602667817870689 chr14 107349540 372490 0.0034698797964108647 0.8023041346306841 chr15 102531392 317291 0.0030945741963592966 0.46168960168765477 chr16 90354753 221789 0.002454646741162582 0.39719905317236975 chr17 81195210 401053 0.004939367728712075 0.8320955407238897 chr18 78077248 222111 0.0028447595898871848 0.614239568644619 chr19 59128983 222635 0.003765243180319878 0.7264633480006425 chr20 63025520 343125 0.005444223228939642 1.1221865242395739 chr21 48129895 68534 0.0014239382820178603 0.24134152603746906 chr22 51304566 341289 0.006652214931513113 2.3539161917582363 chrMT 16571 81166 4.898074950214229 37.220236148161156 chrX 155270560 935228 0.0060232152186480165 0.6843702169762963 chrY 59373566 87949 0.00148128209109084 0.5007298986533097