BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514733.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 62,164,627 number of mapped reads = 60,916,991 (97.99%) number of supplementary alignments = 1,398,186 (2.25%) number of secondary alignments = 0 number of mapped bases = 5,839,692,360 bp number of sequenced bases = 5,837,308,670 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,256,613 duplication rate = 41.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9894 >>>>>>> ACTG content number of A's = 1,528,589,373 bp (26.19%) number of C's = 1,365,918,367 bp (23.4%) number of T's = 1,545,224,931 bp (26.47%) number of G's = 1,369,295,978 bp (23.46%) number of N's = 28,280,021 bp (0.48%) GC percentage = 46.86% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 48,826,992 number of insertions = 1,765,307 mapped reads with insertion percentage = 2.83% number of deletions = 1,380,821 mapped reads with deletion percentage = 2.22% homopolymer indels = 48.26% >>>>>>> Coverage mean coverageData = 1.8864X std coverageData = 24.6543X There is a 7.17% of reference with a coverageData >= 1X There is a 4.98% of reference with a coverageData >= 2X There is a 4.09% of reference with a coverageData >= 3X There is a 3.61% of reference with a coverageData >= 4X There is a 3.28% of reference with a coverageData >= 5X There is a 3.02% of reference with a coverageData >= 6X There is a 2.82% of reference with a coverageData >= 7X There is a 2.65% of reference with a coverageData >= 8X There is a 2.5% of reference with a coverageData >= 9X There is a 2.37% of reference with a coverageData >= 10X There is a 2.26% of reference with a coverageData >= 11X There is a 2.16% of reference with a coverageData >= 12X There is a 2.07% of reference with a coverageData >= 13X There is a 1.99% of reference with a coverageData >= 14X There is a 1.91% of reference with a coverageData >= 15X There is a 1.84% of reference with a coverageData >= 16X There is a 1.78% of reference with a coverageData >= 17X There is a 1.72% of reference with a coverageData >= 18X There is a 1.66% of reference with a coverageData >= 19X There is a 1.61% of reference with a coverageData >= 20X There is a 1.56% of reference with a coverageData >= 21X There is a 1.52% of reference with a coverageData >= 22X There is a 1.48% of reference with a coverageData >= 23X There is a 1.44% of reference with a coverageData >= 24X There is a 1.4% of reference with a coverageData >= 25X There is a 1.36% of reference with a coverageData >= 26X There is a 1.33% of reference with a coverageData >= 27X There is a 1.3% of reference with a coverageData >= 28X There is a 1.27% of reference with a coverageData >= 29X There is a 1.24% of reference with a coverageData >= 30X There is a 1.21% of reference with a coverageData >= 31X There is a 1.18% of reference with a coverageData >= 32X There is a 1.16% of reference with a coverageData >= 33X There is a 1.13% of reference with a coverageData >= 34X There is a 1.11% of reference with a coverageData >= 35X There is a 1.09% of reference with a coverageData >= 36X There is a 1.06% of reference with a coverageData >= 37X There is a 1.04% of reference with a coverageData >= 38X There is a 1.02% of reference with a coverageData >= 39X There is a 1% of reference with a coverageData >= 40X There is a 0.98% of reference with a coverageData >= 41X There is a 0.97% of reference with a coverageData >= 42X There is a 0.95% of reference with a coverageData >= 43X There is a 0.93% of reference with a coverageData >= 44X There is a 0.92% of reference with a coverageData >= 45X There is a 0.9% of reference with a coverageData >= 46X There is a 0.89% of reference with a coverageData >= 47X There is a 0.87% of reference with a coverageData >= 48X There is a 0.86% of reference with a coverageData >= 49X There is a 0.84% of reference with a coverageData >= 50X There is a 0.83% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 340434426 1.3658318066938737 21.477852843639504 chr2 243199373 331717231 1.3639723939584334 17.158277115672384 chr3 198022430 1017218572 5.136885614422568 54.48171960762793 chr4 191154276 125192400 0.6549285876293973 8.283415859591546 chr5 180915260 583135029 3.223249542354802 26.5343954694583 chr6 171115067 101343476 0.5922533753266742 14.385559395848446 chr7 159138663 270087951 1.6971862519669403 15.686706497008585 chr8 146364022 104987683 0.7173052609882502 10.70948980468975 chr9 141213431 336940886 2.3860399369518897 32.77021312536534 chr10 135534747 323519264 2.3869839370416206 26.386794752705647 chr11 135006516 441914093 3.27327973562402 25.096243844567326 chr12 133851895 287838467 2.150425042544224 24.02382222415783 chr13 115169878 28600361 0.2483319553399197 3.509485366945086 chr14 107349540 93879835 0.874524800013116 11.260834751250028 chr15 102531392 55288659 0.5392364028374842 6.498855692028715 chr16 90354753 201315123 2.228052385910457 22.080791239099234 chr17 81195210 524809482 6.463552246493358 54.15110197895911 chr18 78077248 77153795 0.9881725723734525 12.567004604189302 chr19 59128983 175054212 2.9605483321098216 27.326877792643636 chr20 63025520 97236130 1.5428056761768882 20.74215235496856 chr21 48129895 60032376 1.247299126665454 13.99667494102824 chr22 51304566 190319826 3.7096079518536422 30.64204706903633 chrMT 16571 6213969 374.9905859634301 162.1975982323938 chrX 155270560 61285777 0.39470313625454817 9.634662641018014 chrY 59373566 4173337 0.07028947865452448 2.7491929016263548