BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090126.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 = 23,890,336 number of mapped reads = 20,266,663 (84.83%) number of supplementary alignments = 1,021 (0%) number of secondary alignments = 0 number of mapped bases = 958,664,904 bp number of sequenced bases = 958,488,816 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,085,218 duplication rate = 10.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0437 >>>>>>> ACTG content number of A's = 280,615,345 bp (29.28%) number of C's = 195,402,285 bp (20.39%) number of T's = 275,981,709 bp (28.79%) number of G's = 206,371,618 bp (21.53%) number of N's = 117,859 bp (0.01%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 4,619,363 number of insertions = 35,285 mapped reads with insertion percentage = 0.17% number of deletions = 115,453 mapped reads with deletion percentage = 0.57% homopolymer indels = 46.64% >>>>>>> Coverage mean coverageData = 0.3097X std coverageData = 1.5368X There is a 15.22% of reference with a coverageData >= 1X There is a 6.54% of reference with a coverageData >= 2X There is a 3.3% of reference with a coverageData >= 3X There is a 1.84% of reference with a coverageData >= 4X There is a 1.11% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% 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 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% 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 76022138 0.30500280278138203 2.3373357411722027 chr2 243199373 98384785 0.4045437444446043 1.6142154278256065 chr3 198022430 88428986 0.44656045277295103 1.3711495861413288 chr4 191154276 51219639 0.2679492191950757 0.9884588992682174 chr5 180915260 44516890 0.24606487037080232 0.9251674007038319 chr6 171115067 54938021 0.32105893398621643 1.1790042301592405 chr7 159138663 65210014 0.4097685174092483 2.352504362048328 chr8 146364022 85232164 0.5823300209664913 2.91123535945678 chr9 141213431 31775654 0.22501863863076876 1.2701651345489726 chr10 135534747 29207400 0.21549750633319145 1.1280787659834697 chr11 135006516 37222536 0.2757091813257369 1.2433394769196364 chr12 133851895 34104249 0.25479093142461673 0.959719726484796 chr13 115169878 29652940 0.25747131554658764 0.9739881111543162 chr14 107349540 35558927 0.33124433509449597 1.1307283139854496 chr15 102531392 25999056 0.25357166710464635 0.9521209546600922 chr16 90354753 19305830 0.21366701096510107 0.8779627766958424 chr17 81195210 19610507 0.24152295437132312 0.9904996758654157 chr18 78077248 39407862 0.5047291369695817 2.152322720410226 chr19 59128983 16659837 0.2817541610685237 1.6086768796769557 chr20 63025520 22117224 0.3509248951853154 1.1895059218997073 chr21 48129895 13337797 0.2771208414229867 1.11086542469091 chr22 51304566 7873392 0.1534637677278081 0.7129002783011211 chrMT 16571 1075682 64.913523625611 42.71072959421832 chrX 155270560 29493703 0.18995038724662291 0.8614027168128712 chrY 59373566 2309671 0.03890066161766332 1.1836266283831745