BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238509.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 = 3,716,340 number of mapped reads = 3,297,419 (88.73%) number of supplementary alignments = 26,674 (0.72%) number of secondary alignments = 0 number of mapped bases = 202,134,987 bp number of sequenced bases = 202,000,451 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 945,688 duplication rate = 19.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.2836 >>>>>>> ACTG content number of A's = 50,081,407 bp (24.79%) number of C's = 35,813,793 bp (17.73%) number of T's = 67,427,644 bp (33.38%) number of G's = 48,663,612 bp (24.09%) number of N's = 13,995 bp (0.01%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,317,541 number of insertions = 12,247 mapped reads with insertion percentage = 0.37% number of deletions = 79,204 mapped reads with deletion percentage = 2.37% homopolymer indels = 39.81% >>>>>>> Coverage mean coverageData = 0.0653X std coverageData = 1.0659X There is a 2.95% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 30854285 0.12378819710142266 1.0287555591383495 chr2 243199373 9759673 0.040130337836027236 2.9581032352860097 chr3 198022430 12183597 0.061526348303068495 0.5037392972734447 chr4 191154276 10197647 0.05334773154642902 0.44242985104673754 chr5 180915260 18498185 0.10224778716842349 0.6283767886117453 chr6 171115067 3472885 0.020295611958004844 0.8198054964605664 chr7 159138663 16152078 0.10149688137068237 0.9701439369747622 chr8 146364022 7824738 0.0534608019995515 0.6797147709941705 chr9 141213431 7250834 0.05134663146878713 0.563129989960312 chr10 135534747 15934528 0.11756784405994428 0.7137137040415965 chr11 135006516 5120956 0.037931176595950376 0.3913154955160453 chr12 133851895 1962505 0.014661764781141126 0.24504916790336198 chr13 115169878 1184203 0.010282228483388686 0.5083573060365271 chr14 107349540 5255637 0.04895816973225968 0.44376594157702054 chr15 102531392 9897729 0.09653364503234288 0.8827402041771447 chr16 90354753 6752249 0.07473042397669993 0.5838072160555716 chr17 81195210 4288684 0.052819421244184234 0.4668219688961078 chr18 78077248 10302026 0.1319465819287073 1.5339739224535576 chr19 59128983 2058201 0.03480866565893751 0.6701894577523894 chr20 63025520 7737918 0.12277436187753786 0.7248012226252608 chr21 48129895 6022376 0.12512755325977754 0.7074695944994641 chr22 51304566 408247 0.007957322940808037 0.15191160653538274 chrMT 16571 93510 5.642990767002595 5.727713947327931 chrX 155270560 8443450 0.05437894987948778 0.46855447887751833 chrY 59373566 478846 0.008064969518590141 0.2576797111427976