BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068139.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,681,154 number of mapped reads = 1,494,438 (88.89%) number of supplementary alignments = 14,138 (0.84%) number of secondary alignments = 0 number of mapped bases = 102,020,800 bp number of sequenced bases = 101,974,947 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 123,589 duplication rate = 6.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7543 >>>>>>> ACTG content number of A's = 29,061,151 bp (28.5%) number of C's = 18,541,738 bp (18.18%) number of T's = 32,788,945 bp (32.15%) number of G's = 21,522,299 bp (21.11%) number of N's = 60,814 bp (0.06%) GC percentage = 39.29% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 869,360 number of insertions = 7,887 mapped reads with insertion percentage = 0.52% number of deletions = 27,783 mapped reads with deletion percentage = 1.84% homopolymer indels = 47.71% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.3954X There is a 2.01% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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% 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 6918887 0.027758755313191375 0.7532396007625105 chr2 243199373 14466612 0.05948457770078215 0.5116223880052981 chr3 198022430 11466421 0.057904657568337084 0.3575650008656888 chr4 191154276 2747179 0.014371527843823907 0.19726998996845935 chr5 180915260 3398469 0.018784866461789902 0.20375035582577877 chr6 171115067 12936186 0.07559933924462654 0.5180398208382946 chr7 159138663 8616991 0.05414769005568433 0.4653597275647182 chr8 146364022 1157218 0.007906437553349006 0.33273259208542705 chr9 141213431 6105475 0.04323579532601258 0.3855398662156867 chr10 135534747 2450431 0.01807972534157606 0.38481938695337514 chr11 135006516 3804268 0.028178402885383695 0.31253962109977 chr12 133851895 8446358 0.06310226687489183 0.39038090108376644 chr13 115169878 3718827 0.0322899274061921 0.2730798547969694 chr14 107349540 596078 0.005552683318438067 0.12464237727187483 chr15 102531392 674374 0.006577244167327798 0.12030904398473101 chr16 90354753 2024121 0.02240193163939035 0.23106887515496938 chr17 81195210 647670 0.00797670207392776 0.13598762231888262 chr18 78077248 2098748 0.026880404391302317 0.4206724703692974 chr19 59128983 2009258 0.033980932836270836 0.4864824677955793 chr20 63025520 2683188 0.04257304025417006 0.32578619303138373 chr21 48129895 2761052 0.057366674080631175 0.37369203740923407 chr22 51304566 192533 0.003752745905695801 0.08135857354145434 chrMT 16571 4060 0.2450063363707682 0.6552717787277458 chrX 155270560 1901703 0.01224767270756285 0.18717172723510792 chrY 59373566 194693 0.0032791191959061377 0.11993284990436784