BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084782.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 = 2,429,467 number of mapped reads = 2,198,259 (90.48%) number of supplementary alignments = 23,205 (0.96%) number of secondary alignments = 0 number of mapped bases = 147,675,505 bp number of sequenced bases = 147,613,961 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,231 duplication rate = 3.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9858 >>>>>>> ACTG content number of A's = 41,386,541 bp (28.04%) number of C's = 27,600,306 bp (18.7%) number of T's = 46,398,094 bp (31.43%) number of G's = 32,180,547 bp (21.8%) number of N's = 48,473 bp (0.03%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,307,860 number of insertions = 11,962 mapped reads with insertion percentage = 0.54% number of deletions = 38,198 mapped reads with deletion percentage = 1.72% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 0.0477X std coverageData = 0.4049X There is a 4.08% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.08% 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 11794025 0.04731793627105948 0.6964282804939386 chr2 243199373 11997875 0.04933349478660046 0.4766064086934063 chr3 198022430 10282163 0.05192423403752797 0.25694681663240726 chr4 191154276 10135356 0.05302186386874234 0.2779733713580383 chr5 180915260 9040624 0.04997159443598069 0.2548090854603711 chr6 171115067 9016126 0.05269042731345218 0.3242154845509413 chr7 159138663 8492645 0.0533663211686025 0.5001175684106371 chr8 146364022 7351545 0.05022781486559586 0.4865331357614624 chr9 141213431 6444837 0.04563898033183543 0.39286950031928725 chr10 135534747 6841891 0.050480715472911164 0.38210554763423543 chr11 135006516 6105194 0.045221476569323515 0.3674760039557921 chr12 133851895 6076895 0.04540014170139317 0.2464522708809606 chr13 115169878 4645318 0.040334487460340976 0.2284392549486297 chr14 107349540 4642025 0.04324215082803336 0.2573925078092305 chr15 102531392 4366104 0.04258309494130344 0.23685999287940018 chr16 90354753 4159688 0.04603729036811157 0.28533037247288534 chr17 81195210 3887271 0.04787561975638711 0.2919666763246165 chr18 78077248 4184005 0.053588018368680206 0.8700665640522133 chr19 59128983 2810049 0.047524054320366035 0.4743846220985936 chr20 63025520 3000157 0.04760225699050163 0.2698075181226013 chr21 48129895 2055404 0.04270534976234625 0.2505015809785299 chr22 51304566 1630757 0.031785806354935345 0.19782058076664527 chrMT 16571 3744 0.225936877677871 0.5535743232924818 chrX 155270560 8322652 0.053600965952592686 0.30974475672613727 chrY 59373566 389155 0.006554347771531863 0.1467596568702777