BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008795.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 = 1,437,471 number of mapped reads = 1,190,203 (82.8%) number of supplementary alignments = 12,937 (0.9%) number of secondary alignments = 0 number of mapped bases = 77,552,191 bp number of sequenced bases = 77,520,777 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 169,996 duplication rate = 10.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8152 >>>>>>> ACTG content number of A's = 20,460,407 bp (26.39%) number of C's = 14,522,638 bp (18.73%) number of T's = 24,281,942 bp (31.32%) number of G's = 18,226,546 bp (23.51%) number of N's = 29,244 bp (0.04%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 616,719 number of insertions = 5,584 mapped reads with insertion percentage = 0.46% number of deletions = 17,969 mapped reads with deletion percentage = 1.49% homopolymer indels = 46.3% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2894X There is a 1.38% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 6448302 0.025870756005057255 0.3349436095602696 chr2 243199373 7642029 0.031422897624000044 0.3483698736803404 chr3 198022430 5909389 0.029842018401652782 0.2821497612271936 chr4 191154276 2825171 0.014779533364976885 0.19986001701405756 chr5 180915260 2426907 0.013414606374277107 0.18388482765602052 chr6 171115067 4645638 0.027149204809650104 0.2751921472247984 chr7 159138663 5094851 0.0320151678036908 0.36225300184965464 chr8 146364022 6206041 0.042401410641749106 0.40456270339994743 chr9 141213431 2321244 0.016437841525145012 0.23809597867125581 chr10 135534747 4775077 0.03523138608876438 0.32895461477283633 chr11 135006516 3441381 0.025490480770572584 0.3232921918943277 chr12 133851895 2614705 0.019534314400255597 0.22447676016220405 chr13 115169878 1539247 0.013365013723466825 0.18567319224439235 chr14 107349540 3145285 0.029299473477017227 0.28104718936825024 chr15 102531392 1808943 0.017642821039628526 0.21407443057647121 chr16 90354753 2538195 0.028091438642967682 0.274682837516623 chr17 81195210 3287787 0.040492376335993216 0.35214231740050944 chr18 78077248 1122949 0.014382538175525858 0.33928406401585987 chr19 59128983 1867279 0.03157975844096625 0.3121263894546302 chr20 63025520 2015669 0.03198179086820704 0.2963647286307666 chr21 48129895 984897 0.020463310796751167 0.23520990695520888 chr22 51304566 1298377 0.025307240684971394 0.2563987433138623 chrMT 16571 29966 1.808339870858729 2.971867241521889 chrX 155270560 3343419 0.021532858514840162 0.24713951393667924 chrY 59373566 219443 0.0036959713688074587 0.10976158971349542