BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237313.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 = 2,415,371 number of mapped reads = 2,182,173 (90.35%) number of supplementary alignments = 10,537 (0.44%) number of secondary alignments = 0 number of mapped bases = 148,431,851 bp number of sequenced bases = 148,375,902 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,759 duplication rate = 2.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7968 >>>>>>> ACTG content number of A's = 42,128,131 bp (28.39%) number of C's = 27,305,887 bp (18.4%) number of T's = 46,641,318 bp (31.43%) number of G's = 32,297,929 bp (21.77%) number of N's = 2,637 bp (0%) GC percentage = 40.17% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,121,440 number of insertions = 11,388 mapped reads with insertion percentage = 0.52% number of deletions = 32,012 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.88% >>>>>>> Coverage mean coverageData = 0.0479X std coverageData = 0.4784X There is a 4.11% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.07% 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 0.01% 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 9364047 0.037568801082345143 0.67051980152729 chr2 243199373 10380940 0.04268489623120862 0.5651294880449482 chr3 198022430 10696075 0.05401446189706893 0.26077193164573415 chr4 191154276 10791081 0.05645220826762986 0.2911209217135083 chr5 180915260 7810623 0.04317282577489594 0.23509793649193012 chr6 171115067 10717930 0.06263580518014816 0.39731233898907686 chr7 159138663 7868423 0.049443817433605056 0.7527935231637995 chr8 146364022 6825291 0.04663230011539311 0.7896362439465017 chr9 141213431 5400585 0.03824413132487377 0.49634389456774 chr10 135534747 6838970 0.05045916380395058 0.39163640780073056 chr11 135006516 7911489 0.05860079375724354 0.5715439173118996 chr12 133851895 7013823 0.05239987823855613 0.2651217436310814 chr13 115169878 5793188 0.050301242830178214 0.25275163618799 chr14 107349540 4868764 0.04535430706084069 0.27457355501181335 chr15 102531392 4752284 0.04634955116965544 0.25766465082670825 chr16 90354753 4436440 0.049100239364275614 0.2965025949198742 chr17 81195210 4103971 0.05054449640563772 0.3200932480265014 chr18 78077248 3865698 0.04951119691103867 1.0058827203019487 chr19 59128983 2100733 0.035527974496026765 0.49621999527122884 chr20 63025520 2930831 0.0465022898660733 0.26973505810703624 chr21 48129895 2178345 0.045259708129427666 0.26777961949112206 chr22 51304566 1760727 0.03431910914127994 0.2054079272997421 chrMT 16571 10161 0.6131796511978758 0.8549689089678184 chrX 155270560 9614185 0.06191891753336885 0.3381468958727291 chrY 59373566 397247 0.006690637378930549 0.14580116501520607