BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708624.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,299,578 number of mapped reads = 2,392,799 (72.52%) number of supplementary alignments = 789 (0.02%) number of secondary alignments = 0 number of mapped bases = 116,737,045 bp number of sequenced bases = 116,713,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,764 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5852 >>>>>>> ACTG content number of A's = 34,383,822 bp (29.46%) number of C's = 22,112,019 bp (18.95%) number of T's = 36,706,518 bp (31.45%) number of G's = 23,501,182 bp (20.14%) number of N's = 10,293 bp (0.01%) GC percentage = 39.08% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 765,415 number of insertions = 5,737 mapped reads with insertion percentage = 0.24% number of deletions = 15,225 mapped reads with deletion percentage = 0.63% homopolymer indels = 48.58% >>>>>>> Coverage mean coverageData = 0.0377X std coverageData = 0.3719X There is a 3.26% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 9191167 0.03687520200802228 0.6611798621338504 chr2 243199373 10063621 0.04138012724235107 0.4021587674869426 chr3 198022430 8049782 0.04065085960211679 0.22952938388811997 chr4 191154276 8075919 0.04224817340732676 0.2356921965491112 chr5 180915260 7594942 0.04198065989568818 0.23428065935772543 chr6 171115067 7157765 0.04183012709219814 0.31890202170285425 chr7 159138663 6765788 0.04251504865288456 0.6126272721206794 chr8 146364022 6291305 0.04298395817518597 0.5677840000523676 chr9 141213431 4974295 0.03522536747938657 0.29098331473185957 chr10 135534747 5348341 0.03946103208500474 0.30207339238548336 chr11 135006516 5367178 0.039754955234901405 0.29227240150357714 chr12 133851895 5303854 0.039624795749062795 0.23387538098102284 chr13 115169878 4062026 0.035269864573443416 0.21667544963003837 chr14 107349540 3278713 0.030542403814678664 0.21814795248294516 chr15 102531392 3071513 0.0299568058141647 0.19540258169039046 chr16 90354753 2539772 0.02810889206902043 0.20225419123002783 chr17 81195210 2791664 0.03438212672890433 0.2396216959434059 chr18 78077248 3228512 0.041350227917869235 0.5718567320014559 chr19 59128983 1774569 0.030011830238987874 0.5063029207388748 chr20 63025520 2246079 0.03563761155798476 0.22425410796799033 chr21 48129895 1364753 0.028355619724497634 0.20404726378020824 chr22 51304566 1160091 0.02261184706250122 0.16837636415972843 chrMT 16571 1973 0.11906342405407036 0.4029107677121044 chrX 155270560 6767133 0.043582846613034694 0.2633472037727731 chrY 59373566 266290 0.004484992530177487 0.08348570117976527