BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716718.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 = 1,591,713 number of mapped reads = 1,468,359 (92.25%) number of supplementary alignments = 27,827 (1.75%) number of secondary alignments = 0 number of mapped bases = 113,905,529 bp number of sequenced bases = 113,862,998 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,487 duplication rate = 5.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.561 >>>>>>> ACTG content number of A's = 28,508,082 bp (25.04%) number of C's = 22,290,273 bp (19.58%) number of T's = 33,926,887 bp (29.8%) number of G's = 29,133,251 bp (25.59%) number of N's = 4,505 bp (0%) GC percentage = 45.16% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 744,080 number of insertions = 9,488 mapped reads with insertion percentage = 0.64% number of deletions = 20,673 mapped reads with deletion percentage = 1.38% homopolymer indels = 38.68% >>>>>>> Coverage mean coverageData = 0.0368X std coverageData = 0.3079X There is a 2.88% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 11695500 0.046922651398328914 0.5334762748170002 chr2 243199373 11428598 0.046992711613610946 0.33848316014992225 chr3 198022430 7754498 0.03915969519210526 0.2450786340569108 chr4 191154276 5450742 0.02851488396733537 0.2700295640784032 chr5 180915260 7048295 0.038959096098361186 0.24636754644643294 chr6 171115067 6929930 0.04049865462753201 0.259141897972218 chr7 159138663 6677859 0.04196251793318133 0.3577929616277517 chr8 146364022 6501938 0.044423061836876825 0.31354566894794644 chr9 141213431 4376519 0.030992229060704573 0.239473732698962 chr10 135534747 4678359 0.03451778310398883 0.3544350130231749 chr11 135006516 4961945 0.03675337418528747 0.268972697967115 chr12 133851895 4072717 0.03042704027462592 0.2147351165465929 chr13 115169878 2059837 0.017885206060563857 0.1642734106155637 chr14 107349540 2334290 0.021744760154538155 0.18573661548345818 chr15 102531392 2161381 0.02108018781213855 0.17722418845997762 chr16 90354753 4496231 0.04976197544361612 0.2987123674715344 chr17 81195210 2700899 0.03326426521958623 0.24187513343575792 chr18 78077248 3628875 0.046478008548661964 0.32901393338712803 chr19 59128983 3116600 0.0527084999922965 0.4412761699406305 chr20 63025520 2126836 0.03374563192814593 0.2379318865321908 chr21 48129895 1663192 0.03455631889494045 0.2755057642974149 chr22 51304566 1924104 0.03750356254840943 0.24988607092536042 chrMT 16571 248195 14.977671836340596 11.23161305923668 chrX 155270560 5531521 0.03562504701470775 0.23833891059268206 chrY 59373566 336668 0.005670334842276443 0.20534330887285754