BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695913.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 12,875,388 number of mapped reads = 11,535,658 (89.59%) number of supplementary alignments = 169,122 (1.31%) number of secondary alignments = 0 number of mapped bases = 1,509,422,484 bp number of sequenced bases = 1,499,128,793 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,192,579 duplication rate = 16.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.085 >>>>>>> ACTG content number of A's = 425,477,969 bp (28.38%) number of C's = 322,301,376 bp (21.5%) number of T's = 420,342,345 bp (28.04%) number of G's = 331,007,103 bp (22.08%) number of N's = 0 bp (0%) GC percentage = 43.58% >>>>>>> Mismatches and indels general error rate = 0.0173 number of mismatches = 16,039,763 number of insertions = 9,037,794 mapped reads with insertion percentage = 47.43% number of deletions = 9,296,275 mapped reads with deletion percentage = 48.72% homopolymer indels = 36.3% >>>>>>> Coverage mean coverageData = 0.4876X std coverageData = 1.3534X There is a 22.37% of reference with a coverageData >= 1X There is a 11.17% of reference with a coverageData >= 2X There is a 5.92% of reference with a coverageData >= 3X There is a 3.31% of reference with a coverageData >= 4X There is a 1.95% of reference with a coverageData >= 5X There is a 1.19% of reference with a coverageData >= 6X There is a 0.75% of reference with a coverageData >= 7X There is a 0.49% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 171761020 0.6891096973435424 2.0207044364148374 chr2 243199373 115097051 0.47326212062232575 1.2507815772880997 chr3 198022430 103675655 0.5235551093883658 1.2823847381825733 chr4 191154276 61651662 0.32252305985559016 0.9943521147752736 chr5 180915260 127244985 0.7033402544373537 1.594206641832053 chr6 171115067 74904666 0.43774442141906766 1.2167256426260158 chr7 159138663 91370310 0.5741553201310985 1.3498312004342583 chr8 146364022 68588190 0.4686137280376184 1.221787076537138 chr9 141213431 61873100 0.43815308191187563 1.2417602590188044 chr10 135534747 61238610 0.4518295961403905 1.3250059545334645 chr11 135006516 79060263 0.5856033126578868 1.3840652161398934 chr12 133851895 73556363 0.5495354623107876 1.366636583186677 chr13 115169878 44066155 0.38261875210113533 1.0857701943296483 chr14 107349540 33744827 0.314345333943676 0.969475873019187 chr15 102531392 57293163 0.5587865519274331 1.378986791571985 chr16 90354753 51242931 0.5671304419370169 1.3628959165284034 chr17 81195210 41282314 0.508432874303792 1.3379808392279382 chr18 78077248 25725891 0.32949279923390745 1.2812981729717219 chr19 59128983 29396521 0.4971592526798575 1.692197983397278 chr20 63025520 45474561 0.7215261532153959 1.6400505019816083 chr21 48129895 12194518 0.2533668107939982 0.9381065114057927 chr22 51304566 14245002 0.27765563790170256 0.9531002990691808 chrMT 16571 194814 11.756321284171142 7.00257199199724 chrX 155270560 62761867 0.40420970337197215 1.1070178244616786 chrY 59373566 1778045 0.02994674431379109 0.596244136681284