BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714243.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 = 292,438 number of mapped reads = 35,922 (12.28%) number of supplementary alignments = 1,150 (0.39%) number of secondary alignments = 0 number of mapped bases = 3,517,463 bp number of sequenced bases = 3,494,265 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,745 duplication rate = 37.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.9968 >>>>>>> ACTG content number of A's = 350,563 bp (10.03%) number of C's = 227,120 bp (6.5%) number of T's = 289,713 bp (8.29%) number of G's = 2,626,615 bp (75.17%) number of N's = 254 bp (0.01%) GC percentage = 81.67% >>>>>>> Mismatches and indels general error rate = 0.0319 number of mismatches = 91,849 number of insertions = 3,490 mapped reads with insertion percentage = 7.71% number of deletions = 4,248 mapped reads with deletion percentage = 11.11% homopolymer indels = 44.17% >>>>>>> Coverage mean coverageData = 0.0011X std coverageData = 3.0617X There is a 0.01% 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 86861 3.4848860015478155E-4 0.1517242928796515 chr2 243199373 2488442 0.01023210697175605 10.91499728235513 chr3 198022430 45362 2.2907505983034345E-4 0.06000980722175326 chr4 191154276 30408 1.5907569862575296E-4 0.035541909369192534 chr5 180915260 113768 6.288468977133272E-4 0.19856862462974692 chr6 171115067 33688 1.9687337059570565E-4 0.03863722513020206 chr7 159138663 40737 2.559843047066444E-4 0.09705466594484845 chr8 146364022 34555 2.3608944006745045E-4 0.051912266711690205 chr9 141213431 34811 2.4651337874511385E-4 0.04030258135847393 chr10 135534747 52043 3.8398271404158817E-4 0.08090833072592837 chr11 135006516 28038 2.0767886492234196E-4 0.04966526755872332 chr12 133851895 34176 2.5532697912121455E-4 0.06220972758130906 chr13 115169878 28950 2.513678099059895E-4 0.0530661334941361 chr14 107349540 77268 7.197795165214495E-4 0.4009179319565289 chr15 102531392 17488 1.7056239712419003E-4 0.03574994458029169 chr16 90354753 27770 3.073440973271212E-4 0.07690791395768899 chr17 81195210 62362 7.680502335051538E-4 0.28350406280297064 chr18 78077248 9474 1.2134136694981872E-4 0.021632338318564672 chr19 59128983 14089 2.382757031352966E-4 0.04481159602757834 chr20 63025520 20097 3.188708320058288E-4 0.04796030724204682 chr21 48129895 3801 7.897378541964407E-5 0.017447644705663554 chr22 51304566 5386 1.0498090949643742E-4 0.034181920334842554 chrMT 16571 9484 0.5723251463399915 4.069379569766667 chrX 155270560 210429 0.001355240813197299 0.1257658542871759 chrY 59373566 7976 1.343358760024621E-4 0.03462999040159761