BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153371.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 43,367,754 number of mapped reads = 43,048,183 (99.26%) number of supplementary alignments = 364,821 (0.84%) number of secondary alignments = 0 number of mapped bases = 4,170,334,016 bp number of sequenced bases = 4,169,593,739 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,232,087 duplication rate = 31.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.2056 >>>>>>> ACTG content number of A's = 1,118,000,718 bp (26.81%) number of C's = 961,178,952 bp (23.05%) number of T's = 1,140,636,922 bp (27.36%) number of G's = 948,106,821 bp (22.74%) number of N's = 1,670,326 bp (0.04%) GC percentage = 45.79% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 11,238,932 number of insertions = 462,031 mapped reads with insertion percentage = 1.06% number of deletions = 350,577 mapped reads with deletion percentage = 0.8% homopolymer indels = 49.81% >>>>>>> Coverage mean coverageData = 1.3471X std coverageData = 12.418X There is a 20.5% of reference with a coverageData >= 1X There is a 10.22% of reference with a coverageData >= 2X There is a 5.54% of reference with a coverageData >= 3X There is a 4.1% of reference with a coverageData >= 4X There is a 3.29% of reference with a coverageData >= 5X There is a 2.87% of reference with a coverageData >= 6X There is a 2.59% of reference with a coverageData >= 7X There is a 2.38% of reference with a coverageData >= 8X There is a 2.22% of reference with a coverageData >= 9X There is a 2.08% of reference with a coverageData >= 10X There is a 1.96% of reference with a coverageData >= 11X There is a 1.85% of reference with a coverageData >= 12X There is a 1.76% of reference with a coverageData >= 13X There is a 1.68% of reference with a coverageData >= 14X There is a 1.6% of reference with a coverageData >= 15X There is a 1.53% of reference with a coverageData >= 16X There is a 1.47% of reference with a coverageData >= 17X There is a 1.41% of reference with a coverageData >= 18X There is a 1.36% of reference with a coverageData >= 19X There is a 1.3% of reference with a coverageData >= 20X There is a 1.26% of reference with a coverageData >= 21X There is a 1.21% of reference with a coverageData >= 22X There is a 1.17% of reference with a coverageData >= 23X There is a 1.13% of reference with a coverageData >= 24X There is a 1.09% of reference with a coverageData >= 25X There is a 1.06% of reference with a coverageData >= 26X There is a 1.02% of reference with a coverageData >= 27X There is a 0.99% of reference with a coverageData >= 28X There is a 0.96% of reference with a coverageData >= 29X There is a 0.93% of reference with a coverageData >= 30X There is a 0.91% of reference with a coverageData >= 31X There is a 0.88% of reference with a coverageData >= 32X There is a 0.86% of reference with a coverageData >= 33X There is a 0.83% of reference with a coverageData >= 34X There is a 0.81% of reference with a coverageData >= 35X There is a 0.79% of reference with a coverageData >= 36X There is a 0.77% of reference with a coverageData >= 37X There is a 0.75% of reference with a coverageData >= 38X There is a 0.73% of reference with a coverageData >= 39X There is a 0.71% of reference with a coverageData >= 40X There is a 0.69% of reference with a coverageData >= 41X There is a 0.67% of reference with a coverageData >= 42X There is a 0.66% of reference with a coverageData >= 43X There is a 0.64% of reference with a coverageData >= 44X There is a 0.63% of reference with a coverageData >= 45X There is a 0.61% of reference with a coverageData >= 46X There is a 0.6% of reference with a coverageData >= 47X There is a 0.58% of reference with a coverageData >= 48X There is a 0.57% of reference with a coverageData >= 49X There is a 0.56% of reference with a coverageData >= 50X There is a 0.54% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 456194810 1.830265490090795 17.327668306974882 chr2 243199373 301172370 1.2383764245971145 10.032969518560087 chr3 198022430 219538849 1.1086564739156064 9.176658620084016 chr4 191154276 165221689 0.8643368720666234 7.1511909819478445 chr5 180915260 262049887 1.4484675698445781 12.305867329553966 chr6 171115067 140571489 0.8215026967788874 7.187956904487145 chr7 159138663 205129531 1.2889987080009588 15.288422290879783 chr8 146364022 227173653 1.5521140366038861 17.352999816911918 chr9 141213431 103558344 0.7333462778055438 6.670712587602677 chr10 135534747 203615072 1.5023090130533094 11.56574466092346 chr11 135006516 191819902 1.420819584737673 10.558052336992649 chr12 133851895 212382366 1.5866967441887916 12.557225322960583 chr13 115169878 53929077 0.46825678672682103 4.713350235003215 chr14 107349540 119104061 1.109497637344324 9.51187805742244 chr15 102531392 193691426 1.889093888435651 14.333571451291578 chr16 90354753 194976994 2.157905229401712 18.345521207997574 chr17 81195210 163773127 2.01702941589781 13.225780351590423 chr18 78077248 46795407 0.5993475461635123 5.5065500962440295 chr19 59128983 216599255 3.663165574824786 24.363984546988952 chr20 63025520 101118251 1.6044016931554075 12.196078395685278 chr21 48129895 45828795 0.9521897980454768 8.959784399944796 chr22 51304566 56193034 1.0952832931088434 9.609069632011655 chrMT 16571 8323 0.5022629895600749 1.3873891086810144 chrX 155270560 286993559 1.8483449728010255 15.840507715485879 chrY 59373566 2894745 0.04875477750485797 1.8747921713605185