BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237311.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 = 2,446,044 number of mapped reads = 2,028,367 (82.92%) number of supplementary alignments = 16,932 (0.69%) number of secondary alignments = 0 number of mapped bases = 134,277,079 bp number of sequenced bases = 134,223,682 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,960 duplication rate = 6.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4504 >>>>>>> ACTG content number of A's = 36,545,417 bp (27.23%) number of C's = 24,634,575 bp (18.35%) number of T's = 42,723,871 bp (31.83%) number of G's = 30,317,687 bp (22.59%) number of N's = 2,132 bp (0%) GC percentage = 40.94% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,059,151 number of insertions = 9,587 mapped reads with insertion percentage = 0.47% number of deletions = 30,884 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.26% >>>>>>> Coverage mean coverageData = 0.0434X std coverageData = 0.4338X There is a 3.11% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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% 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 6721487 0.026966781358590878 0.3050475779824191 chr2 243199373 7569874 0.031126206891988986 0.45212721067900835 chr3 198022430 3543252 0.01789318513059354 0.17342908694525472 chr4 191154276 5336732 0.02791845472502012 0.2639678486698893 chr5 180915260 7971671 0.04406301049452655 0.27480762249919355 chr6 171115067 18630388 0.10887637381458641 0.7276213808902838 chr7 159138663 9823129 0.061726853894706904 0.9409260762183058 chr8 146364022 7425681 0.05073433278568964 0.5490330112211207 chr9 141213431 7897941 0.05592910634683184 0.416265158087912 chr10 135534747 8925833 0.06585641835447555 0.43767229612559977 chr11 135006516 4981887 0.03690108557426962 0.35110690165697644 chr12 133851895 4388282 0.032784608690074955 0.24367602392853596 chr13 115169878 5444367 0.04727249081569749 0.28531998604773173 chr14 107349540 7170913 0.06679966211313063 0.36442623561359416 chr15 102531392 3192335 0.03113519613583321 0.24117089965037114 chr16 90354753 1414384 0.015653675684332843 0.20632754314030613 chr17 81195210 1514987 0.01865857604161625 0.19702019479635097 chr18 78077248 3482209 0.04459953557789332 0.721259520187646 chr19 59128983 1441946 0.024386450211734575 0.31428119672659877 chr20 63025520 914755 0.014514041296287599 0.18561651890475633 chr21 48129895 1013574 0.021059135907111372 0.22993832276276338 chr22 51304566 1187555 0.023147160040297387 0.19775724723242408 chrMT 16571 215532 13.006577756321285 8.796432102343228 chrX 155270560 13692943 0.08818763196320023 0.43013195476394406 chrY 59373566 375422 0.006323049553735748 0.16997585190979364