BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094001.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 433,806 number of mapped reads = 102,141 (23.55%) number of supplementary alignments = 230 (0.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 49,690 number of mapped paired reads (second in pair) = 52,451 number of mapped paired reads (both in pair) = 97,936 number of mapped paired reads (singletons) = 4,205 number of mapped bases = 14,018,979 bp number of sequenced bases = 13,985,364 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,885 duplication rate = 37.48% >>>>>>> Insert size mean insert size = 8,138.6547 std insert size = 875,640.3416 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 7.6344 >>>>>>> ACTG content number of A's = 3,999,822 bp (28.6%) number of C's = 2,740,609 bp (19.6%) number of T's = 4,044,326 bp (28.92%) number of G's = 3,200,427 bp (22.88%) number of N's = 180 bp (0%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0183 number of mismatches = 249,649 number of insertions = 2,227 mapped reads with insertion percentage = 1.92% number of deletions = 10,405 mapped reads with deletion percentage = 9.95% homopolymer indels = 16.76% >>>>>>> Coverage mean coverageData = 0.0045X std coverageData = 11.1092X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 3811 1.5289831514602326E-5 0.008085526124202002 chr2 243199373 371739 0.0015285360131253299 1.5714041636203653 chr3 198022430 2163 1.0923005035338674E-5 0.0045591014032508115 chr4 191154276 2738 1.4323509038322532E-5 0.004775835095771304 chr5 180915260 2673 1.4774873053826415E-5 0.004873523815465527 chr6 171115067 2433 1.4218502453673469E-5 0.00903326404950556 chr7 159138663 1273123 0.008000086063309455 9.533403685129871 chr8 146364022 1697 1.1594379389219025E-5 0.004743265125961466 chr9 141213431 1724 1.2208470453493903E-5 0.007000263443069686 chr10 135534747 4548 3.35559707061688E-5 0.034586677222715384 chr11 135006516 2471 1.8302820287577825E-5 0.013253598012911531 chr12 133851895 3263 2.4377689983395455E-5 0.019535930370726783 chr13 115169878 879 7.632203969166312E-6 0.003298412134123562 chr14 107349540 2670 2.4872020876847724E-5 0.022015398037606725 chr15 102531392 1178 1.1489164216165132E-5 0.006374270664860822 chr16 90354753 1816 2.0098555302342533E-5 0.006544522015850531 chr17 81195210 2293 2.8240582172273463E-5 0.028213591598749404 chr18 78077248 832 1.0656113289238883E-5 0.0037806647236104467 chr19 59128983 588 9.944361803077181E-6 0.0032744813175402915 chr20 63025520 601 9.535819775862222E-6 0.004048468245991262 chr21 48129895 360 7.479758682207805E-6 0.002975061650984053 chr22 51304566 336 6.549124691942624E-6 0.0025591173870903993 chrMT 16571 12226424 737.820529841289 4647.301319890289 chrX 155270560 108164 6.966162806394206E-4 0.7079821297315896 chrY 59373566 455 7.663342976569741E-6 0.004740026644217796