BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234058.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 = 2,970,193 number of mapped reads = 2,698,566 (90.85%) number of supplementary alignments = 17,889 (0.6%) number of secondary alignments = 0 number of mapped bases = 177,661,937 bp number of sequenced bases = 177,584,026 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 196,892 duplication rate = 5.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.3593 >>>>>>> ACTG content number of A's = 46,622,392 bp (26.25%) number of C's = 33,122,174 bp (18.65%) number of T's = 56,157,677 bp (31.62%) number of G's = 41,665,352 bp (23.46%) number of N's = 16,431 bp (0.01%) GC percentage = 42.11% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,182,136 number of insertions = 14,596 mapped reads with insertion percentage = 0.54% number of deletions = 45,544 mapped reads with deletion percentage = 1.67% homopolymer indels = 44.32% >>>>>>> Coverage mean coverageData = 0.0574X std coverageData = 0.6379X There is a 4.73% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 9618634 0.03859021077423915 0.758020100125491 chr2 243199373 10747468 0.04419200537988229 0.7668609846494175 chr3 198022430 28475428 0.14379900297153206 0.44616627275052473 chr4 191154276 7311286 0.03824809024936486 0.2652946372845061 chr5 180915260 5498533 0.030392864593069707 0.23332975131143183 chr6 171115067 23126798 0.1351534870976616 0.8103252825625852 chr7 159138663 11747866 0.0738215703119235 1.4585419502355994 chr8 146364022 7891557 0.05391732812589695 0.3919540598699253 chr9 141213431 12064659 0.08543563395184414 0.708597354183171 chr10 135534747 8922353 0.06583074228190355 0.5620900264201717 chr11 135006516 7349142 0.05443546147061524 0.48321797349968315 chr12 133851895 1962847 0.014664319843958877 0.2384036336707851 chr13 115169878 7139570 0.06199164333576875 0.29966702874896534 chr14 107349540 6613267 0.06160498684950117 0.48829941008368694 chr15 102531392 3823231 0.03728839456310122 0.2583459713495959 chr16 90354753 2680930 0.029671156314267165 0.4176972350690225 chr17 81195210 1780556 0.02192932317066487 0.21293905662874502 chr18 78077248 926793 0.011870205773646121 1.4081580083425649 chr19 59128983 3102444 0.052469091173105414 0.542332244091766 chr20 63025520 2497253 0.03962288609439478 0.31579782282173097 chr21 48129895 1487726 0.030910642959017468 0.32233076023054863 chr22 51304566 544400 0.010611141316349893 0.1191002936584608 chrMT 16571 47989 2.8959628266248263 2.5157723034995665 chrX 155270560 11834511 0.07621864054589614 0.45465921308358137 chrY 59373566 466696 0.007860332997347674 0.17653549414853273