BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716595.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 = 2,245,154 number of mapped reads = 2,026,787 (90.27%) number of supplementary alignments = 9,701 (0.43%) number of secondary alignments = 0 number of mapped bases = 116,146,077 bp number of sequenced bases = 116,116,409 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,157 duplication rate = 3.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3576 >>>>>>> ACTG content number of A's = 28,657,933 bp (24.68%) number of C's = 21,965,628 bp (18.92%) number of T's = 37,154,325 bp (32%) number of G's = 28,336,695 bp (24.4%) number of N's = 1,828 bp (0%) GC percentage = 43.32% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 576,555 number of insertions = 7,485 mapped reads with insertion percentage = 0.37% number of deletions = 18,951 mapped reads with deletion percentage = 0.93% homopolymer indels = 41.06% >>>>>>> Coverage mean coverageData = 0.0375X std coverageData = 0.3626X There is a 3.22% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11055233 0.04435388347537959 0.5867950611612198 chr2 243199373 9277225 0.03814658272165858 0.44325437091142744 chr3 198022430 10512546 0.053087652747216565 0.262497395553906 chr4 191154276 5164155 0.0270156394513508 0.20305761910464368 chr5 180915260 4898640 0.027076986208902445 0.18838628510948055 chr6 171115067 9409940 0.05499188449606252 0.6405829302098397 chr7 159138663 8195331 0.05149805110528043 0.5555609487349531 chr8 146364022 10501120 0.07174659357201868 0.3497794555148895 chr9 141213431 4038936 0.028601642006701188 0.24834849766602263 chr10 135534747 6530924 0.04818634442133131 0.3766327343226614 chr11 135006516 3664878 0.027145934200687026 0.26799396334565123 chr12 133851895 4850866 0.0362405478084565 0.22061362250877667 chr13 115169878 2508130 0.021777656133316385 0.1681837948660488 chr14 107349540 2390893 0.022272037681763703 0.1926853914574157 chr15 102531392 3252493 0.031721923759700836 0.20808437684018005 chr16 90354753 2382731 0.026370842937283 0.20953700875850895 chr17 81195210 2351957 0.028966696434432525 0.20439803105542473 chr18 78077248 2115727 0.02709786851093932 0.45516586530650455 chr19 59128983 2193021 0.037088765758071636 0.41563532366550066 chr20 63025520 1711881 0.027161711636809978 0.18975872826887852 chr21 48129895 1031813 0.02143808956990245 0.1887457734575891 chr22 51304566 1757223 0.034250811126635396 0.21026093748346522 chrMT 16571 108903 6.571902721622111 4.002569957503529 chrX 155270560 5953030 0.03833972132257396 0.2551298642686775 chrY 59373566 288481 0.004858744714777616 0.11764286969936252