BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716744.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 = 924,802 number of mapped reads = 718,302 (77.67%) number of supplementary alignments = 1,012 (0.11%) number of secondary alignments = 0 number of mapped bases = 38,230,229 bp number of sequenced bases = 38,220,803 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,100 duplication rate = 5.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2699 >>>>>>> ACTG content number of A's = 7,737,070 bp (20.24%) number of C's = 6,485,462 bp (16.97%) number of T's = 12,975,342 bp (33.95%) number of G's = 11,022,190 bp (28.84%) number of N's = 739 bp (0%) GC percentage = 45.81% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 251,453 number of insertions = 2,337 mapped reads with insertion percentage = 0.32% number of deletions = 5,584 mapped reads with deletion percentage = 0.77% homopolymer indels = 39.84% >>>>>>> Coverage mean coverageData = 0.0123X std coverageData = 0.1365X There is a 1.09% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.02% 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 3710664 0.014887280862582083 0.16367619878561046 chr2 243199373 3318623 0.013645688963186594 0.18024716994031825 chr3 198022430 2647251 0.013368440130746805 0.12886052310757337 chr4 191154276 2355129 0.012320566661035613 0.12733197456525436 chr5 180915260 2439194 0.013482522148767329 0.1289566693035808 chr6 171115067 1847470 0.010796652991404901 0.1289125195529311 chr7 159138663 2188750 0.013753728721473549 0.14263543403799092 chr8 146364022 2314154 0.01581094840369992 0.14453582260520909 chr9 141213431 1678610 0.011887042104373201 0.1291625356967 chr10 135534747 1930793 0.014245741721124841 0.14652933892005615 chr11 135006516 1652234 0.012238179674231428 0.13241366668899066 chr12 133851895 1774079 0.013254044703662956 0.12968102359749575 chr13 115169878 652369 0.005664406451832831 0.08418456251816119 chr14 107349540 1209780 0.011269540605390578 0.11944071072705499 chr15 102531392 727172 0.00709218889762074 0.0942287888536892 chr16 90354753 992358 0.010982908668899798 0.12288639256879046 chr17 81195210 1494145 0.0184018860225868 0.1579891874509421 chr18 78077248 996813 0.012767009923300576 0.13947970734621923 chr19 59128983 1043751 0.017652104721638796 0.17348264465109411 chr20 63025520 997044 0.015819687009325747 0.1469839073805136 chr21 48129895 518567 0.010774322279323486 0.11949001578179405 chr22 51304566 425935 0.00830208757637673 0.10534734968069331 chrMT 16571 55643 3.357854082433166 3.1707359601940066 chrX 155270560 1153850 0.007431221990826851 0.09878003219707626 chrY 59373566 105851 0.0017827967415667773 0.05793560315935908