BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084888.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,476,485 number of mapped reads = 2,203,449 (88.97%) number of supplementary alignments = 14,179 (0.57%) number of secondary alignments = 0 number of mapped bases = 153,101,706 bp number of sequenced bases = 153,041,487 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,485 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3283 >>>>>>> ACTG content number of A's = 44,562,506 bp (29.12%) number of C's = 28,164,597 bp (18.4%) number of T's = 48,672,448 bp (31.8%) number of G's = 31,618,216 bp (20.66%) number of N's = 23,720 bp (0.02%) GC percentage = 39.06% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,273,960 number of insertions = 12,046 mapped reads with insertion percentage = 0.54% number of deletions = 34,390 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.9% >>>>>>> Coverage mean coverageData = 0.0495X std coverageData = 0.4145X There is a 4.23% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.08% 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% 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 13658196 0.0547970390011586 0.8764207024888252 chr2 243199373 12882755 0.052971991009203793 0.4796440456640952 chr3 198022430 11782038 0.05949850226562718 0.27374114960974627 chr4 191154276 8497987 0.04445617005187998 0.23829013308486163 chr5 180915260 7850029 0.04339064045785856 0.23965462886583078 chr6 171115067 9560708 0.055872975814572776 0.2736108892055535 chr7 159138663 8678408 0.054533623925192835 0.4329873986688152 chr8 146364022 8154760 0.05571560475428859 0.5571122674491312 chr9 141213431 11901675 0.08428146611634979 0.4610436043398111 chr10 135534747 4595868 0.03390914951130576 0.26305348836044684 chr11 135006516 6524046 0.048323934231441094 0.35245033748105953 chr12 133851895 6841264 0.05111069962812256 0.25746405095301556 chr13 115169878 3583276 0.03111296167214834 0.19587666749451096 chr14 107349540 3026013 0.028188411426821203 0.19544140575267513 chr15 102531392 3920946 0.03824141975952106 0.21771291870625975 chr16 90354753 3395027 0.03757441515002537 0.23414839176449176 chr17 81195210 3788485 0.04665897163145461 0.25421498685788996 chr18 78077248 6572322 0.08417717284297725 0.635428341886098 chr19 59128983 2922205 0.04942085677340333 0.5392741590708188 chr20 63025520 2796853 0.04437651605254506 0.23855436215896753 chr21 48129895 1325009 0.02752985436598189 0.1943980865571636 chr22 51304566 1418262 0.027643972273345026 0.18340235065934354 chrMT 16571 17372 1.0483374570031982 1.2048966328918191 chrX 155270560 9107674 0.0586567988162083 0.3021405863150684 chrY 59373566 300528 0.005061646457280332 0.11985730767980356