BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082900.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 = 2,072,568 number of mapped reads = 1,874,805 (90.46%) number of supplementary alignments = 21,418 (1.03%) number of secondary alignments = 0 number of mapped bases = 125,569,415 bp number of sequenced bases = 125,522,292 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,703 duplication rate = 4.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8928 >>>>>>> ACTG content number of A's = 34,961,312 bp (27.85%) number of C's = 22,872,172 bp (18.22%) number of T's = 40,403,246 bp (32.19%) number of G's = 27,279,640 bp (21.73%) number of N's = 5,922 bp (0%) GC percentage = 39.95% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 907,427 number of insertions = 10,286 mapped reads with insertion percentage = 0.54% number of deletions = 28,857 mapped reads with deletion percentage = 1.52% homopolymer indels = 48.55% >>>>>>> Coverage mean coverageData = 0.0406X std coverageData = 0.361X There is a 3.25% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 12360847 0.049592040936178854 0.6953673830953626 chr2 243199373 11999679 0.049340912568882324 0.45272763590302606 chr3 198022430 7812465 0.039452424657146164 0.23677370430170794 chr4 191154276 7769387 0.04064458908572885 0.24882209215549012 chr5 180915260 6408274 0.03542141221254636 0.2255945990785084 chr6 171115067 7087120 0.041417276247216736 0.31303677963305154 chr7 159138663 6367789 0.04001409135880449 0.2965050461951334 chr8 146364022 10080021 0.06886952723941954 0.4463856836845903 chr9 141213431 3630892 0.025712086834006605 0.29501524212846925 chr10 135534747 5344755 0.03943457392516474 0.28944862850858255 chr11 135006516 6005238 0.04448109749013892 0.3333015550787215 chr12 133851895 4917364 0.036737350636686913 0.2381835558401163 chr13 115169878 3242248 0.02815187491993349 0.2007794058543819 chr14 107349540 2406214 0.022414758367851412 0.21393562838407318 chr15 102531392 2825664 0.02755901334100682 0.19739408781932863 chr16 90354753 5537116 0.061281956025047185 0.3139607011269517 chr17 81195210 2576399 0.03173092353600662 0.23401199960111851 chr18 78077248 3858424 0.04941803276672866 0.6603345329311604 chr19 59128983 2304322 0.038971108297262615 0.4497754588014375 chr20 63025520 3095620 0.049116929142353764 0.29036806004207133 chr21 48129895 3451163 0.07170518448045649 0.329565094325091 chr22 51304566 1343100 0.026178956469488507 0.1917013411555745 chrMT 16571 19080 1.1514090881660732 1.3703263955867209 chrX 155270560 4875710 0.03140138091857207 0.23381341083667806 chrY 59373566 250524 0.004219453485411336 0.08658598120079847