BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081106.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,489,775 number of mapped reads = 2,259,884 (90.77%) number of supplementary alignments = 21,937 (0.88%) number of secondary alignments = 0 number of mapped bases = 152,151,294 bp number of sequenced bases = 152,096,761 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,069 duplication rate = 3.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0483 >>>>>>> ACTG content number of A's = 41,852,849 bp (27.52%) number of C's = 28,924,309 bp (19.02%) number of T's = 47,154,623 bp (31%) number of G's = 34,163,272 bp (22.46%) number of N's = 1,708 bp (0%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,371,713 number of insertions = 12,013 mapped reads with insertion percentage = 0.53% number of deletions = 33,450 mapped reads with deletion percentage = 1.46% homopolymer indels = 46.42% >>>>>>> Coverage mean coverageData = 0.0491X std coverageData = 0.3786X There is a 4.16% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% 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 12615151 0.050612315224683034 0.5670420880127152 chr2 243199373 10688766 0.04395063140232685 0.4474296500660508 chr3 198022430 12788231 0.06457970948038563 0.290364366485097 chr4 191154276 9201350 0.048135726767629304 0.27147515306733155 chr5 180915260 8515592 0.0470695064639655 0.24846317836605866 chr6 171115067 12679027 0.07409649671586196 0.4349611888417119 chr7 159138663 7766592 0.048803928935861426 0.3468048003699769 chr8 146364022 10835474 0.0740309937643009 0.4442782532565407 chr9 141213431 7804833 0.055269763964590594 0.4608166157451472 chr10 135534747 6795793 0.05014059604951342 0.36011238811700874 chr11 135006516 7065949 0.052337836790040566 0.38479059339964083 chr12 133851895 7619748 0.05692670992816351 0.28578446072525104 chr13 115169878 3926898 0.03409657167475683 0.21079947590214013 chr14 107349540 4424163 0.04121268707811883 0.2989644946219156 chr15 102531392 3981255 0.038829620103080234 0.223976507880914 chr16 90354753 3643153 0.04032054628050392 0.2904833907919413 chr17 81195210 3517572 0.04332240781198792 0.24998456423624668 chr18 78077248 3783508 0.04845852148887215 0.7253991959326476 chr19 59128983 3302304 0.05584915945535542 0.4416143076454077 chr20 63025520 2500285 0.03967099359116751 0.23936232282019432 chr21 48129895 2126112 0.044174457475961666 0.29889135579359216 chr22 51304566 1367059 0.026645951941197593 0.1845205195449438 chrMT 16571 345899 20.87375535574196 10.231090670068257 chrX 155270560 4474227 0.02881568147883282 0.22845141785853249 chrY 59373566 382353 0.006439785004660155 0.16311564233996198