BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549116.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,202,628 number of mapped reads = 6,096,789 (59.76%) number of secondary alignments = 0 number of mapped bases = 241,933,554 bp number of sequenced bases = 241,910,128 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 162,970 duplication rate = 1.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1554 >>>>>>> ACTG content number of A's = 72,404,133 bp (29.93%) number of C's = 48,234,019 bp (19.94%) number of T's = 72,753,930 bp (30.07%) number of G's = 48,508,033 bp (20.05%) number of N's = 10,013 bp (0%) GC percentage = 39.99% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 745,884 number of insertions = 6,389 mapped reads with insertion percentage = 0.1% number of deletions = 18,791 mapped reads with deletion percentage = 0.31% homopolymer indels = 46.48% >>>>>>> Coverage mean coverageData = 0.0782X std coverageData = 0.5055X There is a 6.78% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.02% 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% 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 18501842 0.07422987323269296 0.8674414985310177 chr2 243199373 20485180 0.08423204281863013 0.4574201355379166 chr3 198022430 16581861 0.08373728673059916 0.32283383817972666 chr4 191154276 16291383 0.08522635925758731 0.32825127719963826 chr5 180915260 20108558 0.11114904292761152 0.37680664657311524 chr6 171115067 14473058 0.08458085108309019 0.36610196504855336 chr7 159138663 17272400 0.10853679221874574 0.8930377849920027 chr8 146364022 12434477 0.08495583019712317 0.6478194852179364 chr9 141213431 10040102 0.07109877529992172 0.43950810130622187 chr10 135534747 11022345 0.08132486498093364 0.4143270856501952 chr11 135006516 10850859 0.08037285400358009 0.4599056281423277 chr12 133851895 10909401 0.08150352297963358 0.33479297797552743 chr13 115169878 7985364 0.06933552538798382 0.28856806166548216 chr14 107349540 7322577 0.06821246742184456 0.3665383792426473 chr15 102531392 6793419 0.06625696645179655 0.2841880399777902 chr16 90354753 6153941 0.06810865832370766 0.32324989120526254 chr17 81195210 5502174 0.06776476100006391 0.31988301357619114 chr18 78077248 6649655 0.08516764064225214 0.8992647078075642 chr19 59128983 3682637 0.062281419587412824 0.7735370282246906 chr20 63025520 4720552 0.07489905676303821 0.32051888563245384 chr21 48129895 3089877 0.06419870643806723 0.3113811305632805 chr22 51304566 2159455 0.04209089304059214 0.2309280669902974 chrMT 16571 32951 1.9884738398406856 2.6820398334889273 chrX 155270560 7956555 0.0512431654783753 0.3145446514697073 chrY 59373566 912931 0.015376051355918222 0.15824394157406896