BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083614.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 = 1,693,804 number of mapped reads = 1,512,579 (89.3%) number of supplementary alignments = 12,999 (0.77%) number of secondary alignments = 0 number of mapped bases = 98,855,880 bp number of sequenced bases = 98,817,817 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,790 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0221 >>>>>>> ACTG content number of A's = 26,164,122 bp (26.48%) number of C's = 18,257,597 bp (18.48%) number of T's = 31,176,513 bp (31.55%) number of G's = 23,215,071 bp (23.49%) number of N's = 4,514 bp (0%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 725,176 number of insertions = 7,510 mapped reads with insertion percentage = 0.49% number of deletions = 23,699 mapped reads with deletion percentage = 1.55% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.0319X std coverageData = 0.3118X There is a 2.81% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 11776892 0.04724919822767463 0.5946732093339986 chr2 243199373 6220837 0.025579165452864882 0.4535128400043145 chr3 198022430 10870118 0.05489336738267478 0.26389703110777335 chr4 191154276 5507487 0.028811738430585775 0.19184441751592038 chr5 180915260 5094578 0.028160023648640807 0.1856071470135835 chr6 171115067 4629471 0.027054724526391356 0.2397973805059517 chr7 159138663 7528712 0.04730913191095491 0.4507551038185676 chr8 146364022 5247318 0.03585114653381143 0.2872191108297725 chr9 141213431 4302306 0.030466691231374445 0.24602815893317334 chr10 135534747 4069305 0.030024071982072614 0.29312138723297665 chr11 135006516 3255730 0.02411535455073887 0.2088139408057885 chr12 133851895 3825628 0.02858105221446435 0.18798272191165732 chr13 115169878 3467591 0.03010848895750328 0.19233904596062482 chr14 107349540 1626729 0.015153572153173643 0.1401769845642641 chr15 102531392 1947524 0.018994416851377576 0.1634412370210875 chr16 90354753 2903532 0.03213480092187292 0.2084878048667091 chr17 81195210 2418884 0.029790969196335598 0.2065470238886415 chr18 78077248 3039029 0.03892336215538744 0.40857762518273627 chr19 59128983 2770516 0.04685546511090847 0.4034142853439082 chr20 63025520 2197103 0.034860529512489545 0.21057719878926057 chr21 48129895 1727558 0.035893658193104305 0.2118809886164362 chr22 51304566 380285 0.007412303224629169 0.09384096048252472 chrMT 16571 1251 0.07549333172409631 0.2946383717051372 chrX 155270560 3837749 0.024716527073773677 0.1846486991830156 chrY 59373566 209747 0.0035326663721023596 0.09133473528418931