BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867839.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,424,993 number of mapped reads = 2,247,732 (92.69%) number of supplementary alignments = 10,248 (0.42%) number of secondary alignments = 0 number of mapped bases = 133,925,491 bp number of sequenced bases = 133,885,708 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,110 duplication rate = 3.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1197 >>>>>>> ACTG content number of A's = 35,039,647 bp (26.17%) number of C's = 27,545,634 bp (20.57%) number of T's = 40,395,990 bp (30.17%) number of G's = 30,885,720 bp (23.07%) number of N's = 18,717 bp (0.01%) GC percentage = 43.64% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 663,116 number of insertions = 8,808 mapped reads with insertion percentage = 0.39% number of deletions = 25,007 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.92% >>>>>>> Coverage mean coverageData = 0.0433X std coverageData = 0.4017X There is a 3.78% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 10805636 0.04335249379378678 0.7791426360216752 chr2 243199373 11365848 0.04673469285630107 0.5390683587703898 chr3 198022430 8993469 0.04541641570603896 0.23785797972081826 chr4 191154276 8548156 0.04471862298283089 0.2826222565934572 chr5 180915260 7972918 0.044069903224305124 0.23609956195160564 chr6 171115067 7696556 0.044978832869229456 0.27620124712655236 chr7 159138663 7369280 0.04630728863167589 0.46539287938691465 chr8 146364022 6817089 0.04657626175372524 0.4334280587027409 chr9 141213431 5624925 0.03983279040929188 0.327329551727823 chr10 135534747 6563645 0.048427765907144094 0.42157050800412615 chr11 135006516 6085344 0.0450744466289316 0.3281797974250239 chr12 133851895 6073119 0.045371931417183146 0.24378192964754827 chr13 115169878 4214147 0.03659070473270797 0.21521837746467523 chr14 107349540 3992274 0.0371894839977889 0.23044411113202146 chr15 102531392 3874106 0.03778458406182567 0.21621280343935703 chr16 90354753 3857699 0.04269503121767153 0.2579181144595306 chr17 81195210 3673464 0.04524237328778385 0.259805506570499 chr18 78077248 3566312 0.045676712375928005 0.6361350902122672 chr19 59128983 2757732 0.046639259802591225 0.5690345828050416 chr20 63025520 2821994 0.044775417957678094 0.24295658554501234 chr21 48129895 1753924 0.03644146740814622 0.261673130272351 chr22 51304566 1633979 0.03184860778278487 0.1991209859027034 chrMT 16571 28377 1.712449459899825 1.5558342270325713 chrX 155270560 7387647 0.04757918693666076 0.2767238697157992 chrY 59373566 447851 0.007542935858021396 0.2911188130355386