BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004086.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 = 2,936,269 number of mapped reads = 2,618,147 (89.17%) number of supplementary alignments = 30,977 (1.05%) number of secondary alignments = 0 number of mapped bases = 171,816,069 bp number of sequenced bases = 171,700,552 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 164,263 duplication rate = 4.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0331 >>>>>>> ACTG content number of A's = 48,597,368 bp (28.3%) number of C's = 30,414,368 bp (17.71%) number of T's = 55,538,110 bp (32.35%) number of G's = 37,074,670 bp (21.59%) number of N's = 76,036 bp (0.04%) GC percentage = 39.31% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,545,185 number of insertions = 13,465 mapped reads with insertion percentage = 0.51% number of deletions = 68,634 mapped reads with deletion percentage = 2.58% homopolymer indels = 43.76% >>>>>>> Coverage mean coverageData = 0.0555X std coverageData = 0.5474X There is a 4.26% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 12190888 0.04891016099013049 1.0319144902049204 chr2 243199373 10813088 0.04446182515445877 0.5465352386549601 chr3 198022430 8700234 0.043935598608703066 0.25898993353053185 chr4 191154276 14139938 0.07397134030106656 0.3497899669104451 chr5 180915260 8943588 0.049435232826683606 0.2792744412052594 chr6 171115067 9350096 0.05464215491906391 0.36374544122437874 chr7 159138663 14083737 0.08849978210511923 0.8601097644623107 chr8 146364022 11390528 0.07782327818239376 0.9071665848751779 chr9 141213431 5796865 0.041050379974125834 0.46352194320926154 chr10 135534747 6847617 0.05052296294174659 0.4480105789908838 chr11 135006516 7882979 0.05838961876477133 0.42952020396107754 chr12 133851895 8504941 0.06353993718206231 0.3221958170841267 chr13 115169878 6068229 0.05268937594949957 0.2815740974499746 chr14 107349540 4558056 0.042459949059865554 0.279173777796453 chr15 102531392 3695476 0.03604238592605863 0.23639496527707204 chr16 90354753 5384101 0.059588464593556024 0.36041342674504245 chr17 81195210 3531454 0.043493378488706415 0.30539557551642127 chr18 78077248 5340174 0.06839603260606726 0.8873526290753941 chr19 59128983 1761434 0.02978968875551267 0.7292490486778287 chr20 63025520 4608429 0.07312004724435435 0.3637746020101231 chr21 48129895 2893415 0.06011679435411193 0.32589713103572754 chr22 51304566 984068 0.019180904873067242 0.1656611772431596 chrMT 16571 7599 0.45857220445356345 0.7824081153367816 chrX 155270560 13823272 0.08902699906537337 0.4263204396238922 chrY 59373566 515863 0.00868842878664219 0.18163602998816938