BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054633.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 7,798,958 number of mapped reads = 5,507,929 (70.62%) number of supplementary alignments = 144 (0%) number of secondary alignments = 0 number of mapped bases = 258,472,174 bp number of sequenced bases = 258,417,825 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,159,733 duplication rate = 15.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3494 >>>>>>> ACTG content number of A's = 79,004,734 bp (30.57%) number of C's = 49,664,932 bp (19.22%) number of T's = 77,217,259 bp (29.88%) number of G's = 52,479,444 bp (20.31%) number of N's = 51,456 bp (0.02%) GC percentage = 39.53% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,666,240 number of insertions = 12,028 mapped reads with insertion percentage = 0.22% number of deletions = 37,089 mapped reads with deletion percentage = 0.67% homopolymer indels = 46.68% >>>>>>> Coverage mean coverageData = 0.0835X std coverageData = 0.6854X There is a 4.08% of reference with a coverageData >= 1X There is a 1.57% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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% 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 17406248 0.06983432149603351 0.6607586812544426 chr2 243199373 21956761 0.09028296713577465 0.8128357493356254 chr3 198022430 20506627 0.10355709199205362 0.7065969815766955 chr4 191154276 16772129 0.08774132261629344 0.671764205269724 chr5 180915260 15885504 0.0878063243531806 0.6619274979387366 chr6 171115067 14288900 0.08350462791216393 0.6750731645301105 chr7 159138663 13683698 0.08598600580174537 0.7155549218094099 chr8 146364022 14480311 0.09893354119498028 0.7421728159131389 chr9 141213431 9063001 0.0641794547148989 0.5701517452012684 chr10 135534747 10173882 0.07506475073879025 0.6131803337413159 chr11 135006516 13836684 0.10248900875273309 0.7761824817685328 chr12 133851895 14043113 0.10491530956659224 0.8466911075615042 chr13 115169878 9542925 0.08285955638504713 0.633545019849349 chr14 107349540 5757537 0.053633550735289595 0.5371123483191307 chr15 102531392 7220527 0.07042259798833123 0.5621564603332019 chr16 90354753 8444131 0.0934553050020512 0.7025585803834952 chr17 81195210 5576169 0.06867608323200347 0.5359169742493942 chr18 78077248 9763406 0.12504802935677242 0.851962249578635 chr19 59128983 5728912 0.09688839058841922 0.7796190693760825 chr20 63025520 5373962 0.08526644444980383 0.6249557651796832 chr21 48129895 2972047 0.06175053986716572 0.566647430882794 chr22 51304566 3388552 0.06604776658670107 0.538991076352333 chrMT 16571 20513 1.2378854625550662 3.010715033872125 chrX 155270560 12061496 0.07768050814011362 0.7035270990443618 chrY 59373566 525139 0.008844659928291995 0.21805227047451006