BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714210.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 = 141,016 number of mapped reads = 16,226 (11.51%) number of supplementary alignments = 683 (0.48%) number of secondary alignments = 0 number of mapped bases = 1,674,894 bp number of sequenced bases = 1,667,768 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,371 duplication rate = 33.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 9.4636 >>>>>>> ACTG content number of A's = 86,646 bp (5.2%) number of C's = 45,373 bp (2.72%) number of T's = 51,476 bp (3.09%) number of G's = 1,484,242 bp (89%) number of N's = 31 bp (0%) GC percentage = 91.72% >>>>>>> Mismatches and indels general error rate = 0.0388 number of mismatches = 44,910 number of insertions = 2,546 mapped reads with insertion percentage = 10.28% number of deletions = 1,331 mapped reads with deletion percentage = 7.95% homopolymer indels = 67.5% >>>>>>> Coverage mean coverageData = 0.0005X std coverageData = 1.77X There is a 0% of reference with a coverageData >= 1X There is a 0% 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 12462 4.999786941353298E-5 0.09377730114258116 chr2 243199373 1465549 0.0060261216216211215 6.3121833565942245 chr3 198022430 8622 4.354052215196026E-5 0.024896728698464553 chr4 191154276 2522 1.3193531700018053E-5 0.0055334503802666945 chr5 180915260 2982 1.6482855011788393E-5 0.00600506655959273 chr6 171115067 9741 5.692660600132892E-5 0.050635806384531544 chr7 159138663 5857 3.680438109499512E-5 0.029600834037434447 chr8 146364022 2749 1.878193809131591E-5 0.007474436766944868 chr9 141213431 2142 1.5168528834909479E-5 0.007452978879834154 chr10 135534747 10241 7.555995954306832E-5 0.11782111269342983 chr11 135006516 8525 6.314510034463818E-5 0.04670849286074236 chr12 133851895 7947 5.937159126510685E-5 0.03319163034483359 chr13 115169878 751 6.520802253519796E-6 0.002759491945358295 chr14 107349540 11371 1.0592499977177359E-4 0.05661523240347798 chr15 102531392 1516 1.4785715578698082E-5 0.006566451352788479 chr16 90354753 1872 2.0718334540740762E-5 0.005950164874783848 chr17 81195210 3382 4.165270340454812E-5 0.042520426761214515 chr18 78077248 595 7.6206579412225185E-6 0.0036090862933250405 chr19 59128983 1593 2.6941102639969303E-5 0.012949267865573983 chr20 63025520 1257 1.9944301927219324E-5 0.00551793311261284 chr21 48129895 1789 3.717024522908267E-5 0.01999739050722005 chr22 51304566 135 2.6313447422983754E-6 0.0016221398886419206 chrMT 16571 151 0.00911230462856798 0.09471021029435936 chrX 155270560 107848 6.945811234273903E-4 0.14003789710325207 chrY 59373566 3295 5.5496077159994064E-5 0.019175138364807394