BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081101.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 = 2,698,863 number of mapped reads = 2,462,251 (91.23%) number of supplementary alignments = 23,858 (0.88%) number of secondary alignments = 0 number of mapped bases = 166,145,703 bp number of sequenced bases = 166,081,292 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,567 duplication rate = 3.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2606 >>>>>>> ACTG content number of A's = 46,070,399 bp (27.74%) number of C's = 31,511,818 bp (18.97%) number of T's = 51,637,803 bp (31.09%) number of G's = 36,859,473 bp (22.19%) number of N's = 1,799 bp (0%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,559,477 number of insertions = 14,121 mapped reads with insertion percentage = 0.57% number of deletions = 38,495 mapped reads with deletion percentage = 1.55% homopolymer indels = 45.74% >>>>>>> Coverage mean coverageData = 0.0537X std coverageData = 0.4652X There is a 4.49% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.11% 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 0.01% 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 14772947 0.05926944912205454 0.6964371414946755 chr2 243199373 10764902 0.04426369141996102 0.5200032578221151 chr3 198022430 12650389 0.06388361661858205 0.29551633823975226 chr4 191154276 10228311 0.05350814647745573 0.32555503637352234 chr5 180915260 8132360 0.044951210859714104 0.24995757286400777 chr6 171115067 14263839 0.08335817090846828 0.5338222193610378 chr7 159138663 7943512 0.049915663800694364 0.4530486222855789 chr8 146364022 13196962 0.09016534131591437 0.5579917454339114 chr9 141213431 9021220 0.06388358342486558 0.5888881824014078 chr10 135534747 8355129 0.06164566050357551 0.5836262931250765 chr11 135006516 6944778 0.05144031714735902 0.35915913142783495 chr12 133851895 8010466 0.05984574219139744 0.31054745044961996 chr13 115169878 4081074 0.03543525504125306 0.21604562236902083 chr14 107349540 4986078 0.046447129629060356 0.3499330094558775 chr15 102531392 4539342 0.044272704305038595 0.241508238412966 chr16 90354753 3805187 0.04211385537183639 0.35623562724885194 chr17 81195210 3975403 0.048961053244397056 0.269070057221478 chr18 78077248 3738328 0.047879863798478146 1.1023410838567453 chr19 59128983 3374220 0.05706541578771954 0.5237201882002616 chr20 63025520 2731902 0.04334596525344019 0.26963980090023054 chr21 48129895 3142127 0.0652843103023599 0.39528670805497673 chr22 51304566 1470634 0.028664778101816512 0.1924299817984032 chrMT 16571 62433 3.7676060587773823 2.792097400714248 chrX 155270560 5419226 0.034901825561780675 0.2588929904422312 chrY 59373566 534934 0.009009632333688698 0.2394755903315967