BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238610.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 = 4,643,979 number of mapped reads = 2,114,377 (45.53%) number of supplementary alignments = 20,566 (0.44%) number of secondary alignments = 0 number of mapped bases = 129,322,615 bp number of sequenced bases = 129,251,934 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 772,260 duplication rate = 21.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9562 >>>>>>> ACTG content number of A's = 32,064,561 bp (24.81%) number of C's = 23,014,332 bp (17.81%) number of T's = 43,292,765 bp (33.49%) number of G's = 30,874,391 bp (23.89%) number of N's = 5,885 bp (0%) GC percentage = 41.69% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 872,321 number of insertions = 8,919 mapped reads with insertion percentage = 0.42% number of deletions = 42,569 mapped reads with deletion percentage = 1.99% homopolymer indels = 39.89% >>>>>>> Coverage mean coverageData = 0.0418X std coverageData = 0.858X There is a 1.42% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 8546757 0.03428981226088901 0.5745733220574359 chr2 243199373 9883644 0.0406400883278593 2.0174717155255206 chr3 198022430 13241213 0.06686723822144794 0.6665546615967195 chr4 191154276 7853931 0.04108687058614373 0.5202661375869416 chr5 180915260 6305439 0.034852996922426556 0.477483043190999 chr6 171115067 6001334 0.0350719203470259 0.8033260187152998 chr7 159138663 5419628 0.03405601063771662 0.6062143032247397 chr8 146364022 4881860 0.033354235100207894 0.6044608527448271 chr9 141213431 5333683 0.037770366191300885 0.5299486971647296 chr10 135534747 6248322 0.04610125549575859 0.6925746945543798 chr11 135006516 6294950 0.04662700872897128 0.5501586014394467 chr12 133851895 7122336 0.05321057277523041 0.6230146573222917 chr13 115169878 2632033 0.02285348431123631 0.5884813667252605 chr14 107349540 3184989 0.02966933067435594 0.4878308468105919 chr15 102531392 3486783 0.03400698002812641 0.61207472476206 chr16 90354753 5171178 0.057231942186815564 0.658015402276322 chr17 81195210 3672699 0.04523295154972812 0.5619013340795425 chr18 78077248 3286627 0.04209455486955688 1.774202597149171 chr19 59128983 2164107 0.03659976698736726 0.6143504307585158 chr20 63025520 3047241 0.04834931945027982 0.5849392928028121 chr21 48129895 2650721 0.05507431503850154 0.663640888158832 chr22 51304566 1285918 0.025064396802421056 0.39824737616645545 chrMT 16571 672624 40.59042906282059 27.037196399925257 chrX 155270560 10417931 0.06709533990216819 0.6775096444454975 chrY 59373566 516667 0.00870197016631947 0.34938497493095194