BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085135.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 = 1,399,790 number of mapped reads = 1,262,718 (90.21%) number of supplementary alignments = 17,174 (1.23%) number of secondary alignments = 0 number of mapped bases = 84,204,713 bp number of sequenced bases = 84,175,405 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,891 duplication rate = 2.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7251 >>>>>>> ACTG content number of A's = 23,827,521 bp (28.31%) number of C's = 16,070,808 bp (19.09%) number of T's = 25,227,530 bp (29.97%) number of G's = 19,033,614 bp (22.61%) number of N's = 15,932 bp (0.02%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 735,616 number of insertions = 7,516 mapped reads with insertion percentage = 0.59% number of deletions = 18,052 mapped reads with deletion percentage = 1.41% homopolymer indels = 43.77% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.3334X There is a 2.5% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 6750842 0.027084554385122275 0.6083621511318189 chr2 243199373 7159452 0.029438612080632295 0.38103870155561453 chr3 198022430 5560325 0.028079268595986827 0.17578096788382824 chr4 191154276 5446061 0.02849039589362887 0.18539540986310502 chr5 180915260 5081780 0.02808928334735279 0.17808669366391083 chr6 171115067 4893409 0.028597183671733594 0.23318250530713563 chr7 159138663 4680154 0.02940928314824412 0.3370382658873054 chr8 146364022 4337528 0.02963520638972329 0.5818895469919909 chr9 141213431 3570976 0.025287792915392023 0.3081858659929943 chr10 135534747 3913703 0.028876012141742517 0.2884619125873492 chr11 135006516 3865317 0.028630595874350243 0.3560218575426183 chr12 133851895 3775631 0.028207527431718466 0.18246066097447047 chr13 115169878 2598169 0.02255944909484058 0.15788955884522904 chr14 107349540 2532934 0.02359520124632113 0.19923456491978042 chr15 102531392 2371556 0.023130047819891104 0.16782916469018241 chr16 90354753 2362875 0.026151086927325227 0.20492165580017835 chr17 81195210 2243231 0.02762762729476283 0.21410744586401828 chr18 78077248 2284761 0.02926282698898404 0.6552462201050513 chr19 59128983 1762090 0.02980078314555148 0.4135052724663191 chr20 63025520 1664195 0.026405097490667273 0.1790237134587524 chr21 48129895 1086015 0.022564250347938637 0.17680274137998583 chr22 51304566 929323 0.018113845851458914 0.14030083572223898 chrMT 16571 22401 1.3518194436063002 1.4168567912830223 chrX 155270560 5092810 0.03279958544620436 0.23674981561428943 chrY 59373566 219175 0.003691457575581699 0.09108755527330524