BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089603.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 = 9,821,636 number of mapped reads = 7,462,830 (75.98%) number of supplementary alignments = 274 (0%) number of secondary alignments = 0 number of mapped bases = 349,281,609 bp number of sequenced bases = 349,209,463 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,948,659 duplication rate = 29.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1304 >>>>>>> ACTG content number of A's = 112,636,515 bp (32.25%) number of C's = 67,020,795 bp (19.19%) number of T's = 94,038,560 bp (26.93%) number of G's = 75,509,757 bp (21.62%) number of N's = 3,836 bp (0%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,990,385 number of insertions = 16,167 mapped reads with insertion percentage = 0.22% number of deletions = 48,243 mapped reads with deletion percentage = 0.64% homopolymer indels = 45.1% >>>>>>> Coverage mean coverageData = 0.1128X std coverageData = 1.0824X There is a 3.45% of reference with a coverageData >= 1X There is a 1.72% of reference with a coverageData >= 2X There is a 1.19% of reference with a coverageData >= 3X There is a 0.89% of reference with a coverageData >= 4X There is a 0.69% of reference with a coverageData >= 5X There is a 0.55% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% 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 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% 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 26657582 0.10695091507916443 1.1347171496739434 chr2 243199373 27281982 0.11217949151538315 1.1599022674575894 chr3 198022430 24238249 0.12240153299805481 1.0686886572578118 chr4 191154276 23279806 0.12178543157465126 1.093877575531704 chr5 180915260 22019451 0.12171140787128737 1.0574685088238989 chr6 171115067 21107266 0.12335130021016794 1.1437824502162948 chr7 159138663 17579431 0.11046612223957167 1.113983539420383 chr8 146364022 17277152 0.11804234240023823 1.2439206806511263 chr9 141213431 15814119 0.11198735763314185 1.0354990676578202 chr10 135534747 15861216 0.11702693479776076 1.0622343764682853 chr11 135006516 16547597 0.12256887660148195 1.1937286699817942 chr12 133851895 16750555 0.12514245689237347 1.081352823967167 chr13 115169878 11078921 0.09619634224150173 0.9700175097836983 chr14 107349540 12059311 0.11233686702337058 1.090481643841061 chr15 102531392 10647518 0.10384642003104766 0.9549883043331018 chr16 90354753 9196408 0.1017811204685602 0.9829781892802607 chr17 81195210 9644657 0.11878357109982227 1.0365807029730685 chr18 78077248 9571832 0.12259438242495432 1.1307435408382884 chr19 59128983 6735199 0.11390689740089052 1.0898374549124872 chr20 63025520 7218404 0.11453144694403156 1.0342531433702864 chr21 48129895 4247911 0.08825930328748899 0.9444273795803008 chr22 51304566 4083164 0.07958675646920003 0.7983250901783154 chrMT 16571 92358 5.573471727717096 13.939890078357214 chrX 155270560 19437821 0.1251867771971712 1.1136977386189162 chrY 59373566 853699 0.014378435682977168 0.314196050995206