BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081100.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 = 2,293,716 number of mapped reads = 2,099,351 (91.53%) number of supplementary alignments = 21,023 (0.92%) number of secondary alignments = 0 number of mapped bases = 141,133,545 bp number of sequenced bases = 141,081,402 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,409 duplication rate = 3.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7034 >>>>>>> ACTG content number of A's = 39,092,276 bp (27.71%) number of C's = 26,478,995 bp (18.77%) number of T's = 44,175,308 bp (31.31%) number of G's = 31,333,281 bp (22.21%) number of N's = 1,542 bp (0%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,263,498 number of insertions = 11,222 mapped reads with insertion percentage = 0.53% number of deletions = 31,959 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.68% >>>>>>> Coverage mean coverageData = 0.0456X std coverageData = 0.379X There is a 3.89% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.08% 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 0.01% 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 11815797 0.04740528610358006 0.6096013493562956 chr2 243199373 9445550 0.038838710328418485 0.4008671667025412 chr3 198022430 12297242 0.06210024793655951 0.2831914551374555 chr4 191154276 8680933 0.04541322946916448 0.26961225145166723 chr5 180915260 7624459 0.042143813628546314 0.23383464216794186 chr6 171115067 11731870 0.06856129156645219 0.48582872605903044 chr7 159138663 6976147 0.04383690844505838 0.4124692407972461 chr8 146364022 10383854 0.0709453994096992 0.4599225235266 chr9 141213431 6896374 0.04883653028726425 0.4142435859207233 chr10 135534747 6401687 0.047232810343461225 0.38598305638259284 chr11 135006516 6295749 0.04663292696183642 0.29430264205992746 chr12 133851895 7125661 0.053235413663736325 0.2720224025860072 chr13 115169878 3842100 0.03336028540379282 0.20576260811439917 chr14 107349540 3853252 0.0358944435160132 0.2627202496264735 chr15 102531392 3563607 0.034756252992254315 0.21050004160090327 chr16 90354753 3288305 0.036393270866447947 0.2651006713657974 chr17 81195210 3135726 0.038619593446460695 0.22680421058532246 chr18 78077248 3319471 0.04251521518791236 0.686991912935974 chr19 59128983 2887878 0.04884031237269885 0.47407084733092064 chr20 63025520 2335781 0.03706087629265098 0.22883144591698565 chr21 48129895 3036718 0.063094216183102 0.31877258774053047 chr22 51304566 1294485 0.025231379990623058 0.17705751487886964 chrMT 16571 414593 25.019190151469434 12.390600746623461 chrX 155270560 4107663 0.026454873351393852 0.20718560264470728 chrY 59373566 378643 0.006377299285005048 0.1606492774511716