BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818802.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 871,428 number of mapped reads = 840,043 (96.4%) number of supplementary alignments = 7,372 (0.85%) number of secondary alignments = 0 number of mapped bases = 56,925,793 bp number of sequenced bases = 56,901,054 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 284,360 duplication rate = 29.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8347 >>>>>>> ACTG content number of A's = 16,522,621 bp (29.04%) number of C's = 12,232,905 bp (21.5%) number of T's = 16,401,531 bp (28.82%) number of G's = 11,740,353 bp (20.63%) number of N's = 3,644 bp (0.01%) GC percentage = 42.13% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 298,324 number of insertions = 7,210 mapped reads with insertion percentage = 0.85% number of deletions = 14,924 mapped reads with deletion percentage = 1.76% homopolymer indels = 39.85% >>>>>>> Coverage mean coverageData = 0.0184X std coverageData = 0.2761X There is a 1.07% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 4700482 0.0188584565251695 0.34472585733642136 chr2 243199373 5028728 0.02067738883520888 0.45028625638759556 chr3 198022430 3880223 0.0195948660967346 0.21745163422548633 chr4 191154276 3774424 0.019745433264595137 0.2455243167182499 chr5 180915260 3497568 0.0193326311998225 0.22459409064920252 chr6 171115067 3373283 0.019713535804535554 0.2373848310635246 chr7 159138663 3103172 0.01949979936679498 0.24302859380395442 chr8 146364022 2860853 0.01954614912126424 0.23200264137847848 chr9 141213431 2401917 0.017009125711278838 0.2246642620097991 chr10 135534747 2767377 0.020418210541980057 0.3033618744984313 chr11 135006516 2674255 0.01980834021374198 0.23973271727837253 chr12 133851895 2609399 0.0194946735718609 0.22367494752761105 chr13 115169878 1851370 0.01607512339294134 0.19817155227418431 chr14 107349540 1718125 0.016004959126979027 0.22025342327207953 chr15 102531392 1636710 0.015963013551986108 0.19849247147538415 chr16 90354753 1674616 0.01853378980516941 0.3191265101076262 chr17 81195210 1552215 0.019117075995000198 0.22535610858745186 chr18 78077248 1522903 0.019505080404473272 0.281899933876774 chr19 59128983 1106766 0.018717825740381836 0.31078850602274627 chr20 63025520 1246647 0.019780035134973898 0.23470047013323242 chr21 48129895 786394 0.016338992636489233 0.20611558253136755 chr22 51304566 691033 0.013469230009664247 0.19157369675159922 chrMT 16571 90095 5.436907851065114 5.669751053045773 chrX 155270560 1803853 0.01161748241263508 0.1832199321976123 chrY 59373566 573385 0.00965724376400097 0.475729381828048