BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238650.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 = 2,974,303 number of mapped reads = 2,490,304 (83.73%) number of supplementary alignments = 22,220 (0.75%) number of secondary alignments = 0 number of mapped bases = 151,753,706 bp number of sequenced bases = 151,691,187 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,102,195 duplication rate = 20.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.0197 >>>>>>> ACTG content number of A's = 37,949,775 bp (25.02%) number of C's = 26,541,409 bp (17.5%) number of T's = 51,456,074 bp (33.92%) number of G's = 35,740,457 bp (23.56%) number of N's = 3,472 bp (0%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 880,216 number of insertions = 9,190 mapped reads with insertion percentage = 0.37% number of deletions = 37,040 mapped reads with deletion percentage = 1.47% homopolymer indels = 40.72% >>>>>>> Coverage mean coverageData = 0.049X std coverageData = 1.0457X There is a 1.08% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 10958884 0.04396732877146974 0.7560963200946644 chr2 243199373 16166864 0.0664757634880909 2.204187508340287 chr3 198022430 6434441 0.03249349581257032 0.60413152560142 chr4 191154276 6442239 0.03370177813861721 0.6109423319541853 chr5 180915260 8429633 0.046594372415019056 0.730474896880739 chr6 171115067 12397416 0.07245075619203072 1.1243087629941564 chr7 159138663 13348660 0.08388068460773734 1.1044237120091773 chr8 146364022 12039388 0.08225647147083728 1.0815183623207993 chr9 141213431 4734345 0.03352616650182517 0.6248175897600515 chr10 135534747 9824845 0.07248949230709081 0.9360625876777655 chr11 135006516 8821945 0.06534458677535239 0.9089048145120334 chr12 133851895 3268601 0.02441953474024406 0.5201920179387146 chr13 115169878 1812685 0.015739228272864888 0.615595726282928 chr14 107349540 3804253 0.03543800001378674 0.6432420522364325 chr15 102531392 1468177 0.014319292573341831 0.5552726710364904 chr16 90354753 3029343 0.03352721245333934 0.626523625864699 chr17 81195210 2427121 0.02989241606740102 0.5616361525836722 chr18 78077248 10985602 0.14070170608472266 2.6636113492827254 chr19 59128983 2365758 0.04001012498388481 0.7136923443910742 chr20 63025520 1690380 0.026820564114346062 0.5418511928010014 chr21 48129895 3348909 0.06958064213520515 0.8935086370380235 chr22 51304566 3720611 0.07252007550361111 0.9648700335755842 chrMT 16571 18387 1.1095890410958904 3.3670369553847608 chrX 155270560 3909507 0.025178675210548607 0.5134887414726975 chrY 59373566 305712 0.005148958039677118 0.28887831465032476