BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080745.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 6,605,330 number of mapped reads = 5,415,092 (81.98%) number of supplementary alignments = 25,225 (0.38%) number of secondary alignments = 0 number of mapped bases = 348,454,991 bp number of sequenced bases = 348,343,225 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 707,747 duplication rate = 10.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3575 >>>>>>> ACTG content number of A's = 107,870,261 bp (30.97%) number of C's = 69,606,243 bp (19.98%) number of T's = 91,359,167 bp (26.23%) number of G's = 78,713,350 bp (22.6%) number of N's = 794,204 bp (0.23%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 3,591,909 number of insertions = 24,329 mapped reads with insertion percentage = 0.45% number of deletions = 59,946 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.35% >>>>>>> Coverage mean coverageData = 0.1126X std coverageData = 0.718X There is a 6.94% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% 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 0.01% 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 42718193 0.1713865057932995 1.1188784622674857 chr2 243199373 24822530 0.1020665871535779 0.6418178920059995 chr3 198022430 20434690 0.10319381496328471 0.4944032314308634 chr4 191154276 19642003 0.10275471420791027 0.5626399793309026 chr5 180915260 27715468 0.15319585534133495 0.604681375086268 chr6 171115067 23778687 0.13896313993203183 0.7703060092401558 chr7 159138663 23794973 0.14952351962388927 1.0722602070571459 chr8 146364022 16056811 0.109704630827923 0.9822568747174633 chr9 141213431 11463828 0.08118086161365204 0.5559364076537548 chr10 135534747 13988576 0.10321025648131398 0.7962000420954659 chr11 135006516 13931938 0.10319455988331704 0.6527246202940625 chr12 133851895 13722667 0.10252127547391092 0.49413879437987723 chr13 115169878 14252280 0.1237500659677698 0.5416283128036666 chr14 107349540 9037903 0.08419135284603921 0.5170297724357643 chr15 102531392 8534153 0.08323453757459959 0.44479737551849613 chr16 90354753 8746028 0.09679654594374244 0.5385611444712766 chr17 81195210 9978327 0.12289304997179021 0.5727674424447842 chr18 78077248 4693860 0.06011815375459955 0.8750713496810373 chr19 59128983 6640914 0.11231233251551105 1.0284415942599436 chr20 63025520 6382587 0.1012698824222315 0.49975937555313515 chr21 48129895 5801360 0.12053548007948074 0.6123155317647652 chr22 51304566 3695712 0.07203475807591862 0.41011016886694274 chrMT 16571 16052 0.9686802244885644 1.4938355470552505 chrX 155270560 17604320 0.11337835066737699 0.5439030101628449 chrY 59373566 1001131 0.016861560917530202 0.48654014401852386