BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237808.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 = 3,132,557 number of mapped reads = 1,901,199 (60.69%) number of supplementary alignments = 9,128 (0.29%) number of secondary alignments = 0 number of mapped bases = 119,683,244 bp number of sequenced bases = 119,636,488 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 138,852 duplication rate = 6.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9536 >>>>>>> ACTG content number of A's = 32,307,395 bp (27%) number of C's = 23,670,280 bp (19.79%) number of T's = 35,970,339 bp (30.07%) number of G's = 27,585,797 bp (23.06%) number of N's = 102,677 bp (0.09%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 945,192 number of insertions = 8,832 mapped reads with insertion percentage = 0.46% number of deletions = 28,562 mapped reads with deletion percentage = 1.49% homopolymer indels = 46.66% >>>>>>> Coverage mean coverageData = 0.0387X std coverageData = 0.3475X There is a 2.64% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% 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 0.01% 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 10468285 0.041999032772720754 0.5046283988503347 chr2 243199373 10022555 0.041211269899120995 0.3963401898881065 chr3 198022430 7608374 0.03842177878536285 0.2747482519258715 chr4 191154276 7420333 0.03881855616978194 0.2898131493780744 chr5 180915260 7430014 0.04106902867121325 0.285774249256307 chr6 171115067 7086915 0.0414160782229656 0.31843831713597825 chr7 159138663 6125288 0.038490256764316284 0.34865901171200064 chr8 146364022 5703225 0.038966030873352195 0.3152738732636502 chr9 141213431 5057441 0.03581416416403054 0.33190994529895257 chr10 135534747 6036976 0.044541906290642946 0.3727145013841747 chr11 135006516 5994356 0.0444004939731946 0.3677232526719477 chr12 133851895 5504015 0.04112018735334304 0.28574999133036244 chr13 115169878 3493680 0.03033501520249939 0.24185002091644503 chr14 107349540 3677968 0.034261609318493584 0.2755161427233857 chr15 102531392 3359561 0.032766169799001654 0.25382108045187685 chr16 90354753 3574583 0.039561648738058085 0.30374548644408506 chr17 81195210 3088518 0.03803817983844121 0.2973631271295985 chr18 78077248 3143874 0.04026619893160169 0.5335727499780814 chr19 59128983 2266100 0.03832469095570272 0.3780191399515304 chr20 63025520 2638945 0.041871054772733333 0.29752008816697545 chr21 48129895 1558664 0.03238452940734651 0.2714711477252482 chr22 51304566 1341870 0.026154981995169788 0.22883998380670245 chrMT 16571 432417 26.09480417597007 17.047553286774594 chrX 155270560 6288349 0.040499300060487964 0.30563802232020865 chrY 59373566 360938 0.006079102609400284 0.15146530302963004