BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708527.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 = 3,086,424 number of mapped reads = 2,008,771 (65.08%) number of supplementary alignments = 799 (0.03%) number of secondary alignments = 0 number of mapped bases = 95,153,099 bp number of sequenced bases = 95,129,892 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,336 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.8148 >>>>>>> ACTG content number of A's = 26,878,297 bp (28.25%) number of C's = 17,863,752 bp (18.78%) number of T's = 30,041,075 bp (31.58%) number of G's = 20,345,470 bp (21.39%) number of N's = 1,298 bp (0%) GC percentage = 40.17% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 517,516 number of insertions = 5,738 mapped reads with insertion percentage = 0.28% number of deletions = 15,157 mapped reads with deletion percentage = 0.75% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.0307X std coverageData = 0.3112X There is a 2.72% of reference with a coverageData >= 1X There is a 0.25% 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 0.01% 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 7886987 0.031642797792668285 0.4830345356057775 chr2 243199373 8301294 0.03413369819830909 0.4838378179055861 chr3 198022430 6599999 0.033329552616842444 0.21236005952727954 chr4 191154276 6151234 0.03217942140096306 0.21633190301553815 chr5 180915260 5940078 0.032833482371802135 0.20644136049874692 chr6 171115067 5868784 0.03429729539830645 0.30359644249074036 chr7 159138663 5350244 0.03362001350985335 0.33208321612112635 chr8 146364022 4885897 0.03338181701511318 0.43461282214086344 chr9 141213431 4014075 0.028425589347800775 0.2707900230232602 chr10 135534747 4662935 0.03440398202831337 0.2649610905888174 chr11 135006516 4409248 0.032659519930134336 0.297148545464531 chr12 133851895 4512874 0.03371542853390309 0.21317637578410703 chr13 115169878 2964108 0.025736833723137224 0.2370199039454282 chr14 107349540 2938451 0.02737273955715134 0.20160534468112185 chr15 102531392 2774673 0.027061692481459728 0.19710425977145105 chr16 90354753 2615371 0.028945582973371638 0.21144329362840072 chr17 81195210 2546586 0.03136374670377723 0.2410452209471624 chr18 78077248 2521003 0.03228857400301814 0.4296919367299574 chr19 59128983 1867880 0.031589922661108515 0.3563037239812292 chr20 63025520 1973331 0.031310031238139725 0.20946267482295333 chr21 48129895 1309485 0.02720731054991913 0.20617166125553776 chr22 51304566 1042304 0.020316008520567155 0.16717458405474706 chrMT 16571 111098 6.704363043871824 4.540608271360072 chrX 155270560 3233028 0.020821899528152665 0.20015729800947757 chrY 59373566 672132 0.011320391300061041 0.14082195676116643