BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505988.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 5,969,306 number of mapped reads = 4,319,185 (72.36%) number of supplementary alignments = 209 (0%) number of secondary alignments = 0 number of mapped bases = 202,344,174 bp number of sequenced bases = 202,303,773 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 406,291 duplication rate = 7.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3976 >>>>>>> ACTG content number of A's = 60,916,958 bp (30.11%) number of C's = 39,950,751 bp (19.75%) number of T's = 61,095,658 bp (30.2%) number of G's = 40,339,561 bp (19.94%) number of N's = 845 bp (0%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,050,029 number of insertions = 9,394 mapped reads with insertion percentage = 0.22% number of deletions = 29,725 mapped reads with deletion percentage = 0.69% homopolymer indels = 45.41% >>>>>>> Coverage mean coverageData = 0.0654X std coverageData = 0.6714X There is a 4.7% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 15633931 0.0627237394124687 1.1785876690339745 chr2 243199373 17226837 0.07083421633656925 0.5254277399589011 chr3 198022430 14128281 0.07134687216998599 0.3570938958766019 chr4 191154276 13916322 0.07280152079883372 0.36070919739256624 chr5 180915260 12761918 0.07054085984786468 0.3581907211471759 chr6 171115067 12206288 0.07133380019656597 0.44791842571696744 chr7 159138663 11437758 0.07187290495207943 0.9104503956282212 chr8 146364022 10621247 0.0725673348878046 1.0201826546541344 chr9 141213431 8384087 0.05937173922217073 0.481865300982708 chr10 135534747 9409058 0.06942174024200598 0.6224262038446927 chr11 135006516 9245276 0.06848022061394429 0.5523226520920443 chr12 133851895 8950196 0.06686641231340057 0.36968784454542736 chr13 115169878 6820248 0.05921902600261503 0.3235885392491519 chr14 107349540 6403358 0.0596496081864906 1.4754081949749587 chr15 102531392 5519710 0.05383434177895488 0.30599896799165943 chr16 90354753 4958800 0.05488145156016308 0.3579127248462764 chr17 81195210 4411230 0.05432869746872999 0.36311849398653273 chr18 78077248 5551564 0.07110347946689924 0.9958359860507883 chr19 59128983 3201304 0.05414102928169761 0.8446703338150969 chr20 63025520 3860782 0.06125743984341581 0.3615087914730704 chr21 48129895 2650777 0.05507547855651877 0.3311927607912299 chr22 51304566 1807923 0.03523902726318745 0.24711776223963206 chrMT 16571 5570 0.33612938265644804 0.7336724475611693 chrX 155270560 12670465 0.0816024943814204 0.43940197854125135 chrY 59373566 561244 0.00945275882536683 0.14129966027655266