BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080715.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 = 1,931,626 number of mapped reads = 1,721,959 (89.15%) number of supplementary alignments = 12,590 (0.65%) number of secondary alignments = 0 number of mapped bases = 115,949,442 bp number of sequenced bases = 115,906,575 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,715 duplication rate = 4.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0855 >>>>>>> ACTG content number of A's = 32,330,155 bp (27.89%) number of C's = 21,267,241 bp (18.35%) number of T's = 37,104,434 bp (32.01%) number of G's = 25,202,925 bp (21.74%) number of N's = 1,820 bp (0%) GC percentage = 40.09% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 932,786 number of insertions = 8,084 mapped reads with insertion percentage = 0.47% number of deletions = 24,372 mapped reads with deletion percentage = 1.4% homopolymer indels = 47.8% >>>>>>> Coverage mean coverageData = 0.0375X std coverageData = 0.3239X There is a 3.15% of reference with a coverageData >= 1X There is a 0.45% 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% 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 13838025 0.05551851764493698 0.43958851707840774 chr2 243199373 7687179 0.031608547773681966 0.33013428814294093 chr3 198022430 7154836 0.03613144228156376 0.21839695485707877 chr4 191154276 5173802 0.02706610654108517 0.1921523529069059 chr5 180915260 5254090 0.029041718205528932 0.19481535610319597 chr6 171115067 6913021 0.040399838080886236 0.2863167606508019 chr7 159138663 7433150 0.046708636731477376 0.7883502672299771 chr8 146364022 13883239 0.09485417803017192 0.46328175412334494 chr9 141213431 3815871 0.027022011808494336 0.22469758118626 chr10 135534747 5608469 0.04138030375339838 0.3144889638743444 chr11 135006516 4830828 0.0357821840243622 0.23605113686277676 chr12 133851895 3725107 0.027830065461531196 0.1926470384823847 chr13 115169878 2542713 0.022077934301536727 0.16937233639573604 chr14 107349540 2217618 0.02065791804976528 0.17117225796512905 chr15 102531392 2109092 0.020570207415110488 0.16420622850185276 chr16 90354753 2836471 0.03139260421640464 0.20815177761282072 chr17 81195210 1826501 0.02249518167389431 0.18156889267685491 chr18 78077248 3566610 0.04568052910881285 0.3200669742064783 chr19 59128983 1805091 0.03052802379503128 0.2958367395438412 chr20 63025520 2886020 0.04579129216228601 0.24674529834097678 chr21 48129895 1722117 0.03578060995146572 0.22354755223103867 chr22 51304566 1082307 0.021095724696316504 0.1644751807243348 chrMT 16571 25366 1.5307464848228833 1.5338646880844689 chrX 155270560 7752622 0.049929761314701254 0.2696971868237352 chrY 59373566 259297 0.004367212843506822 0.09218468203258877