BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240236.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 = 2,532,768 number of mapped reads = 2,027,994 (80.07%) number of supplementary alignments = 15,001 (0.59%) number of secondary alignments = 0 number of mapped bases = 135,235,553 bp number of sequenced bases = 135,169,498 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 331,676 duplication rate = 11.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0996 >>>>>>> ACTG content number of A's = 37,654,400 bp (27.86%) number of C's = 24,702,406 bp (18.28%) number of T's = 43,558,111 bp (32.22%) number of G's = 29,204,003 bp (21.61%) number of N's = 50,578 bp (0.04%) GC percentage = 39.88% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,162,780 number of insertions = 9,889 mapped reads with insertion percentage = 0.48% number of deletions = 37,400 mapped reads with deletion percentage = 1.82% homopolymer indels = 48.12% >>>>>>> Coverage mean coverageData = 0.0437X std coverageData = 0.5327X There is a 1.75% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 10753278 0.04314243213059036 0.7942764292885887 chr2 243199373 14532424 0.0597551869510782 0.5905068021074479 chr3 198022430 8831923 0.044600619232881854 0.43392604168757526 chr4 191154276 8901094 0.04656497456536102 0.4521467623310799 chr5 180915260 7150060 0.0395215970172997 0.41319248680125253 chr6 171115067 6875556 0.040180891843966025 0.4467305608064452 chr7 159138663 7939140 0.049888190904305886 0.7547618194919706 chr8 146364022 8211559 0.056103671433680606 0.7410437541754362 chr9 141213431 4982649 0.035284526158138596 0.4438194687850892 chr10 135534747 6046855 0.04461479534838398 0.5059649003820048 chr11 135006516 5779424 0.04280848192542055 0.5015778341887024 chr12 133851895 6626970 0.049509721173540355 0.48908913014632044 chr13 115169878 3405611 0.029570327408005068 0.35568308480994654 chr14 107349540 4219371 0.03930497513077373 0.41336081679789133 chr15 102531392 3887145 0.03791175487015723 0.396140996357943 chr16 90354753 4087680 0.045240342807422645 0.4384605268279418 chr17 81195210 3284679 0.04045409821589229 0.4256585306869219 chr18 78077248 3295828 0.042212399699333665 0.6622667100985514 chr19 59128983 2296214 0.03883398434233175 0.5509742538033671 chr20 63025520 2793261 0.04431952326613093 0.4323018715680077 chr21 48129895 2231732 0.046368935564891633 0.44788338473015554 chr22 51304566 1230444 0.023983128519204314 0.3090555660674707 chrMT 16571 21064 1.271136322491099 2.0245292758435625 chrX 155270560 7473092 0.04812948443027448 0.4695559690252746 chrY 59373566 378500 0.00637489080578384 0.14860145592019214