BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231809.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 = 4,130,811 number of mapped reads = 3,824,824 (92.59%) number of supplementary alignments = 31,348 (0.76%) number of secondary alignments = 0 number of mapped bases = 246,502,862 bp number of sequenced bases = 246,414,091 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 412,493 duplication rate = 8.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9766 >>>>>>> ACTG content number of A's = 65,854,227 bp (26.73%) number of C's = 43,702,272 bp (17.74%) number of T's = 80,777,465 bp (32.78%) number of G's = 55,984,237 bp (22.72%) number of N's = 95,890 bp (0.04%) GC percentage = 40.45% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,523,862 number of insertions = 16,757 mapped reads with insertion percentage = 0.43% number of deletions = 51,583 mapped reads with deletion percentage = 1.34% homopolymer indels = 45.26% >>>>>>> Coverage mean coverageData = 0.0796X std coverageData = 0.7648X There is a 5.99% of reference with a coverageData >= 1X There is a 1.33% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 24188857 0.09704632591467044 1.3745114529655031 chr2 243199373 18335043 0.07539099617662254 1.1616388386313248 chr3 198022430 19268397 0.09730411347845797 0.39398815480045224 chr4 191154276 13061574 0.0683300121416065 0.37623210017537206 chr5 180915260 12764440 0.07055480007601349 0.34421355587530744 chr6 171115067 19092679 0.11157801200521986 0.6292905629500345 chr7 159138663 19050217 0.11970828861368529 1.228166275916556 chr8 146364022 13865207 0.09473097835477629 1.2619046084752505 chr9 141213431 8779165 0.06216947593320638 0.5511126456683765 chr10 135534747 9941817 0.07335253298550813 0.5255354714533734 chr11 135006516 5860668 0.04341026028699237 0.4152863191439126 chr12 133851895 7493622 0.055984429656375054 0.3198180264287276 chr13 115169878 5430685 0.04715369239168596 0.3086245317485299 chr14 107349540 9217382 0.08586326499396271 0.399203217612082 chr15 102531392 5913036 0.05767049373522599 0.33212958671076603 chr16 90354753 7326943 0.08109084200584335 0.39252432236597784 chr17 81195210 6164822 0.07592593208392466 0.39096580558570027 chr18 78077248 8503305 0.10890887189056664 1.08062699516928 chr19 59128983 4765057 0.08058750139504345 0.8377686898161427 chr20 63025520 6804834 0.10796950187796943 0.43584022111550313 chr21 48129895 5806413 0.12064046680342852 0.4668604640837859 chr22 51304566 2214226 0.04315845883970639 0.2540402789520496 chrMT 16571 495257 29.886971214772796 18.573079248233533 chrX 155270560 11551754 0.07439758058449715 0.4039360980069549 chrY 59373566 607462 0.010231186046665952 0.2191777366731045