BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238076.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,490,029 number of mapped reads = 1,251,584 (84%) number of supplementary alignments = 5,198 (0.35%) number of secondary alignments = 0 number of mapped bases = 76,435,278 bp number of sequenced bases = 76,384,813 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,472 duplication rate = 8.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4727 >>>>>>> ACTG content number of A's = 19,636,400 bp (25.71%) number of C's = 12,575,544 bp (16.46%) number of T's = 25,585,578 bp (33.5%) number of G's = 18,583,802 bp (24.33%) number of N's = 3,489 bp (0%) GC percentage = 40.79% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 625,614 number of insertions = 6,933 mapped reads with insertion percentage = 0.55% number of deletions = 30,453 mapped reads with deletion percentage = 2.4% homopolymer indels = 47.28% >>>>>>> Coverage mean coverageData = 0.0247X std coverageData = 0.2691X There is a 1.84% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 6630841 0.026603107239600417 0.3414794730443215 chr2 243199373 5901015 0.02426410449668388 0.36659554851446025 chr3 198022430 6289873 0.03176343710154451 0.2576511196123581 chr4 191154276 6492091 0.03396257272319663 0.2535561508020598 chr5 180915260 5112073 0.028256726381179785 0.21794166078682634 chr6 171115067 4376384 0.025575678850068766 0.24761085936991428 chr7 159138663 4599778 0.028904214182068375 0.2946203801276909 chr8 146364022 2955323 0.020191594625624594 0.2978686507127322 chr9 141213431 2895014 0.02050098194979768 0.23173707971013388 chr10 135534747 3750016 0.027668299701773154 0.2959356631124482 chr11 135006516 2663687 0.01973006251046431 0.20752646903168478 chr12 133851895 4648950 0.03473204469761149 0.2731163250339463 chr13 115169878 2337542 0.020296470228092105 0.2164498838096359 chr14 107349540 2134431 0.019883000895951672 0.19572839200171022 chr15 102531392 2698095 0.026314818782524674 0.219638914546862 chr16 90354753 1484079 0.01642502414897864 0.18798655371542036 chr17 81195210 1270717 0.015650147342435593 0.18392363915121815 chr18 78077248 1311217 0.01679384242641339 0.4550552868253297 chr19 59128983 859222 0.014531317070006091 0.23712149265378885 chr20 63025520 1727546 0.027410261747939566 0.22569779738081364 chr21 48129895 731624 0.015201030461421119 0.1778290067623664 chr22 51304566 555064 0.01081899805954893 0.1576515344755937 chrMT 16571 24908 1.503107838995836 1.731347567635887 chrX 155270560 4719793 0.030397217605191866 0.2325810926382848 chrY 59373566 265995 0.004480023989126744 0.1532074530147609