BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053637.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 8,964,738 number of mapped reads = 6,126,599 (68.34%) number of supplementary alignments = 155 (0%) number of secondary alignments = 0 number of mapped bases = 288,392,513 bp number of sequenced bases = 288,339,337 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,515,178 duplication rate = 20.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.988 >>>>>>> ACTG content number of A's = 85,309,640 bp (29.59%) number of C's = 55,338,038 bp (19.19%) number of T's = 85,479,968 bp (29.65%) number of G's = 62,081,435 bp (21.53%) number of N's = 130,256 bp (0.05%) GC percentage = 40.72% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 2,383,324 number of insertions = 13,755 mapped reads with insertion percentage = 0.22% number of deletions = 36,989 mapped reads with deletion percentage = 0.6% homopolymer indels = 46.95% >>>>>>> Coverage mean coverageData = 0.0932X std coverageData = 0.7136X There is a 4.84% of reference with a coverageData >= 1X There is a 1.96% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 22796584 0.09146049028299111 0.766849594372037 chr2 243199373 24721396 0.1016507390419958 1.2791439133467377 chr3 198022430 19860374 0.1002935576540496 0.5880578377779053 chr4 191154276 18709425 0.0978760475125338 0.6038074363138214 chr5 180915260 17952797 0.0992331824302715 0.5825998762285132 chr6 171115067 17160644 0.10028715940017134 0.6859436353524864 chr7 159138663 15587089 0.09794658762465536 0.8550710492817163 chr8 146364022 14867663 0.10158003856986111 0.648182486566801 chr9 141213431 11882251 0.08414391546084593 0.5857957965736401 chr10 135534747 13384822 0.09875564972279766 0.6833961041309327 chr11 135006516 13162253 0.0974934646858082 0.6804983876216341 chr12 133851895 13067631 0.09762753825786329 0.5838474817918475 chr13 115169878 9480880 0.0823208304518652 0.5352702629101163 chr14 107349540 8731768 0.08133959400291794 0.5686125400981427 chr15 102531392 8301701 0.08096740752334661 0.5220734284023255 chr16 90354753 8103652 0.08968705830007637 0.5898005717224247 chr17 81195210 7320220 0.09015581091544686 0.5674670366092344 chr18 78077248 7663735 0.09815580333978985 0.7295801342404767 chr19 59128983 5092888 0.08613183825603765 0.7173429496906368 chr20 63025520 6115424 0.09703091699997081 0.5904303944554242 chr21 48129895 3688073 0.07662748900657274 0.5632452485405807 chr22 51304566 3051460 0.059477357239509636 0.43443400545502164 chrMT 16571 37744 2.277714078812383 3.7581896258706893 chrX 155270560 16943119 0.10911997097196018 0.7073675006950997 chrY 59373566 708920 0.011939993632856749 0.22973027590953193