BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084965.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 = 3,058,631 number of mapped reads = 2,751,750 (89.97%) number of supplementary alignments = 28,296 (0.93%) number of secondary alignments = 0 number of mapped bases = 182,819,258 bp number of sequenced bases = 182,751,466 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,362 duplication rate = 3.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6758 >>>>>>> ACTG content number of A's = 51,952,424 bp (28.43%) number of C's = 33,709,979 bp (18.45%) number of T's = 57,274,564 bp (31.34%) number of G's = 39,790,277 bp (21.77%) number of N's = 24,222 bp (0.01%) GC percentage = 40.22% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,566,198 number of insertions = 14,406 mapped reads with insertion percentage = 0.52% number of deletions = 42,156 mapped reads with deletion percentage = 1.52% homopolymer indels = 46.53% >>>>>>> Coverage mean coverageData = 0.0591X std coverageData = 0.5887X There is a 5.09% of reference with a coverageData >= 1X There is a 0.57% 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 0.01% 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 15415544 0.06184756506584591 1.2166965756436898 chr2 243199373 16764569 0.06893343840981038 0.6551541859493757 chr3 198022430 12117168 0.0611908863051524 0.2880197916733771 chr4 191154276 10247658 0.05360935791988247 0.2695785897103446 chr5 180915260 12295539 0.06796297338322925 0.29812250391357314 chr6 171115067 11377582 0.06649082514750147 0.36690899669970145 chr7 159138663 9999543 0.06283540914252873 0.48285452564497794 chr8 146364022 10214031 0.06978512110032067 0.9555045963099273 chr9 141213431 7682264 0.0544017941182946 0.5404159911897741 chr10 135534747 7344386 0.054188214923218174 0.5950790351125853 chr11 135006516 8793180 0.06513152298515724 0.5149775393447357 chr12 133851895 8787889 0.06565382581994823 0.29883064966946665 chr13 115169878 5862270 0.050901069809243006 0.24954589705793376 chr14 107349540 5817042 0.054187861447752825 0.31723319404603295 chr15 102531392 5151077 0.050239023381248936 0.26100663466294055 chr16 90354753 3903356 0.04320033944423488 0.31281201592404395 chr17 81195210 4579334 0.05639906590548876 0.30968307923251576 chr18 78077248 4418014 0.056585165501734896 1.1567437389594852 chr19 59128983 3208277 0.05425895791239974 0.8290843828758953 chr20 63025520 2807985 0.044553142917345225 0.2600000290320267 chr21 48129895 2589803 0.053808615206827275 0.28799958217451926 chr22 51304566 1776732 0.034631069679061315 0.20643991492488462 chrMT 16571 34043 2.0543720958300646 1.7363368183310335 chrX 155270560 11214500 0.07222553972884493 0.3905320576675779 chrY 59373566 417472 0.007031277184867084 0.13281180175989227