BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231718.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 = 939,124 number of mapped reads = 467,157 (49.74%) number of supplementary alignments = 3,904 (0.42%) number of secondary alignments = 0 number of mapped bases = 30,974,839 bp number of sequenced bases = 30,960,266 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,808 duplication rate = 5.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8373 >>>>>>> ACTG content number of A's = 8,866,304 bp (28.64%) number of C's = 5,387,918 bp (17.4%) number of T's = 10,227,988 bp (33.04%) number of G's = 6,476,673 bp (20.92%) number of N's = 1,383 bp (0%) GC percentage = 38.32% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 249,698 number of insertions = 2,896 mapped reads with insertion percentage = 0.61% number of deletions = 7,951 mapped reads with deletion percentage = 1.68% homopolymer indels = 44.85% >>>>>>> Coverage mean coverageData = 0.01X std coverageData = 0.164X There is a 0.76% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 2207826 0.008857855563778114 0.26287535984229254 chr2 243199373 2558747 0.01052119077626076 0.15163123670159945 chr3 198022430 2008417 0.010142371245520015 0.126164144800037 chr4 191154276 2233727 0.011685467083142833 0.14327784452457976 chr5 180915260 1806676 0.009986310718067675 0.1270634932950557 chr6 171115067 2234351 0.013057593578244047 0.18166040366463962 chr7 159138663 1766495 0.011100350893358956 0.16473797489605008 chr8 146364022 1440019 0.009838613207827808 0.27078809689650163 chr9 141213431 1484960 0.010515713622169551 0.14044370514156473 chr10 135534747 1216565 0.008976037709355816 0.1491275745253569 chr11 135006516 1358917 0.010065566020531928 0.13070316735967355 chr12 133851895 1401087 0.010467442392205206 0.13185214988120403 chr13 115169878 946018 0.008214109595566298 0.11668042818374051 chr14 107349540 892092 0.008310161366317919 0.11802922570329252 chr15 102531392 697251 0.006800366077152254 0.10290120024943215 chr16 90354753 573147 0.006343296627682664 0.1011081341581029 chr17 81195210 656515 0.008085637071447934 0.11265923540083678 chr18 78077248 1215531 0.015568312551180083 0.25822670541075393 chr19 59128983 616279 0.010422621339521432 0.1699470223477019 chr20 63025520 490388 0.007780784672621503 0.11250791345886597 chr21 48129895 539003 0.011198923247183482 0.13710932450950117 chr22 51304566 225939 0.004403877035038168 0.07866473936736637 chrMT 16571 6584 0.3973206203608714 0.75689755488526 chrX 155270560 2302683 0.014830132640727257 0.16081235652195042 chrY 59373566 95622 0.0016105146859462678 0.06336209526952002