BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013287.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,956,498 number of mapped reads = 1,702,947 (87.04%) number of supplementary alignments = 15,137 (0.77%) number of secondary alignments = 0 number of mapped bases = 111,493,279 bp number of sequenced bases = 111,434,957 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 131,446 duplication rate = 6.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3116 >>>>>>> ACTG content number of A's = 30,383,132 bp (27.27%) number of C's = 20,068,758 bp (18.01%) number of T's = 36,031,358 bp (32.33%) number of G's = 24,950,228 bp (22.39%) number of N's = 1,481 bp (0%) GC percentage = 40.4% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 825,917 number of insertions = 7,993 mapped reads with insertion percentage = 0.47% number of deletions = 33,891 mapped reads with deletion percentage = 1.97% homopolymer indels = 46.18% >>>>>>> Coverage mean coverageData = 0.036X std coverageData = 0.3716X There is a 2.59% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 12198780 0.04894182390021006 0.7403754010386526 chr2 243199373 13042781 0.0536299943503555 0.4523814532445587 chr3 198022430 7543034 0.03809181616446177 0.257092687618166 chr4 191154276 4494076 0.023510203873231692 0.2278605810514106 chr5 180915260 4147258 0.022923759996807343 0.2001485462139084 chr6 171115067 2269722 0.013264302435740507 0.170215958276232 chr7 159138663 8300691 0.05216011523233672 0.40561682699173124 chr8 146364022 3977167 0.027173119087968215 0.36705146946505407 chr9 141213431 5157975 0.036526093612157896 0.3334531164068636 chr10 135534747 7921483 0.058446141490196606 0.39235119096200727 chr11 135006516 6063317 0.044911291540920883 0.39594963239644865 chr12 133851895 4459752 0.0333185570514336 0.24336008812248477 chr13 115169878 4898334 0.042531381339138 0.2735890805784751 chr14 107349540 2493223 0.023225278841437047 0.20701027131890562 chr15 102531392 2896036 0.028245359235930398 0.22332144629143688 chr16 90354753 4789286 0.05300535767055885 0.31040732833271795 chr17 81195210 2994659 0.0368822126329866 0.29229619645792904 chr18 78077248 1168342 0.014963923933384537 0.5514418789306621 chr19 59128983 2286021 0.0386615984922318 0.500685051241919 chr20 63025520 1670085 0.02649855169778845 0.21945829552869886 chr21 48129895 1841069 0.038252088436926776 0.27471016408993154 chr22 51304566 892597 0.01739800313289854 0.1657433813185322 chrMT 16571 12698 0.7662784382354716 1.1908517276567427 chrX 155270560 5724842 0.03687010596213474 0.2819553513277918 chrY 59373566 250051 0.004211486977218111 0.11793226613794718