BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084816.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 = 1,958,253 number of mapped reads = 1,812,445 (92.55%) number of supplementary alignments = 17,948 (0.92%) number of secondary alignments = 0 number of mapped bases = 123,032,217 bp number of sequenced bases = 122,985,005 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,523 duplication rate = 3.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6159 >>>>>>> ACTG content number of A's = 34,712,445 bp (28.22%) number of C's = 22,297,904 bp (18.13%) number of T's = 39,603,854 bp (32.2%) number of G's = 26,353,329 bp (21.43%) number of N's = 17,473 bp (0.01%) GC percentage = 39.56% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 948,892 number of insertions = 9,950 mapped reads with insertion percentage = 0.55% number of deletions = 28,809 mapped reads with deletion percentage = 1.58% homopolymer indels = 49.34% >>>>>>> Coverage mean coverageData = 0.0397X std coverageData = 0.2673X There is a 3.34% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 10003418 0.04013397422989771 0.34267537236697826 chr2 243199373 10868175 0.04468833478448154 0.3603011701277685 chr3 198022430 10760866 0.05434165210476409 0.2702353313029849 chr4 191154276 7508884 0.03928179979609768 0.2298471781516825 chr5 180915260 7154488 0.039546072564580786 0.23131742109383197 chr6 171115067 5954376 0.03479749682124719 0.22721125123316374 chr7 159138663 7517424 0.047238200059529216 0.29213354868277824 chr8 146364022 7228625 0.04938799099139268 0.3166330707089786 chr9 141213431 9028880 0.06393782755692694 0.3282915919988193 chr10 135534747 4123924 0.0304270608923629 0.20687034362070036 chr11 135006516 4600121 0.03407332576451347 0.24412344716350878 chr12 133851895 4354291 0.03253066383557737 0.20861458484047132 chr13 115169878 3746043 0.03252623919598144 0.20945719425570733 chr14 107349540 2090661 0.019475267430116606 0.1631051195843867 chr15 102531392 2652431 0.025869452742824362 0.19197285421313431 chr16 90354753 1977828 0.021889584491476613 0.17556527274821473 chr17 81195210 3595454 0.044281602326048546 0.24698429310411835 chr18 78077248 4612930 0.059081616196308556 0.3906184425304551 chr19 59128983 2259283 0.03820940062507079 0.267832527404241 chr20 63025520 2490488 0.03951554862220891 0.23096023042282723 chr21 48129895 772578 0.016051936119952058 0.14928296317228057 chr22 51304566 1088366 0.021213823346639363 0.16664278479129763 chrMT 16571 12752 0.7695371432019794 0.9294879423302891 chrX 155270560 8389673 0.05403260605229993 0.27661164448443165 chrY 59373566 240258 0.004046548256845479 0.07642302906101574