BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714202.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 = 112,102 number of mapped reads = 21,947 (19.58%) number of supplementary alignments = 758 (0.68%) number of secondary alignments = 0 number of mapped bases = 2,596,556 bp number of sequenced bases = 2,542,460 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,707 duplication rate = 39.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.448 >>>>>>> ACTG content number of A's = 678,831 bp (26.7%) number of C's = 475,761 bp (18.71%) number of T's = 636,539 bp (25.04%) number of G's = 751,304 bp (29.55%) number of N's = 25 bp (0%) GC percentage = 48.26% >>>>>>> Mismatches and indels general error rate = 0.0422 number of mismatches = 98,006 number of insertions = 2,734 mapped reads with insertion percentage = 11.54% number of deletions = 8,105 mapped reads with deletion percentage = 35.14% homopolymer indels = 30.33% >>>>>>> Coverage mean coverageData = 0.0008X std coverageData = 0.3262X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% 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 172396 6.916572536844351E-4 0.13827120371988671 chr2 243199373 427960 0.0017597084841168566 1.0341171373875733 chr3 198022430 103309 5.217035262116519E-4 0.1116118989011777 chr4 191154276 84149 4.402151066712209E-4 0.094541223989696 chr5 180915260 183082 0.00101197654636762 0.17394130277721676 chr6 171115067 85677 5.00698164703404E-4 0.1440530887856833 chr7 159138663 118478 7.444953838778953E-4 0.15054763474043004 chr8 146364022 110684 7.562240944704293E-4 0.14842902778389105 chr9 141213431 81955 5.803626427007499E-4 0.14317736913073417 chr10 135534747 70456 5.19837175038221E-4 0.13241038499600785 chr11 135006516 74497 5.51802995938359E-4 0.12929635056679079 chr12 133851895 78090 5.834060100531263E-4 0.1282984343443921 chr13 115169878 41156 3.5735038288396904E-4 0.09004939394090591 chr14 107349540 67594 6.296626888200918E-4 0.1348458102961431 chr15 102531392 76385 7.449913486008266E-4 0.15143443237141693 chr16 90354753 46504 5.146823875441284E-4 0.11440412008983306 chr17 81195210 89293 0.00109973236105923 0.2359144848047743 chr18 78077248 37713 4.830216351887812E-4 0.11528231710946517 chr19 59128983 44499 7.525750950257338E-4 0.15730225708121548 chr20 63025520 48933 7.763997821834711E-4 0.17749125358899634 chr21 48129895 33872 7.037621835659521E-4 0.13778401730080106 chr22 51304566 8985 1.7513061118185855E-4 0.044489177210454416 chrMT 16571 27822 1.6789572144107174 13.03035817336774 chrX 155270560 481947 0.0031039174457798053 0.3168703229293367 chrY 59373566 1120 1.8863613480787057E-5 0.005633022337362399