BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082705.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 = 3,877,889 number of mapped reads = 3,587,272 (92.51%) number of supplementary alignments = 16,331 (0.42%) number of secondary alignments = 0 number of mapped bases = 237,556,367 bp number of sequenced bases = 237,464,068 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 164,099 duplication rate = 3.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9383 >>>>>>> ACTG content number of A's = 64,905,438 bp (27.33%) number of C's = 41,387,730 bp (17.43%) number of T's = 78,286,699 bp (32.97%) number of G's = 52,821,118 bp (22.24%) number of N's = 63,083 bp (0.03%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 2,211,586 number of insertions = 21,889 mapped reads with insertion percentage = 0.6% number of deletions = 57,384 mapped reads with deletion percentage = 1.58% homopolymer indels = 48.46% >>>>>>> Coverage mean coverageData = 0.0767X std coverageData = 0.6786X There is a 6.22% of reference with a coverageData >= 1X There is a 0.99% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 22381880 0.08979668700604762 0.9613502061756904 chr2 243199373 25805853 0.10610986649213112 1.0434157379904918 chr3 198022430 16466785 0.08315616064301402 0.3474972190654445 chr4 191154276 13517226 0.0707136993367598 0.33716489738051153 chr5 180915260 13200438 0.07296475709124814 0.32900611406154046 chr6 171115067 14272371 0.0834080320933983 0.6262723455197201 chr7 159138663 12494263 0.07851180074322982 0.8914588020395705 chr8 146364022 19015577 0.12991974899405265 0.7762839028160248 chr9 141213431 7504339 0.0531418218993631 0.785026221188829 chr10 135534747 9414613 0.06946272604175813 0.5519847597993491 chr11 135006516 9749559 0.07221546995553904 0.5937705034212912 chr12 133851895 7275510 0.05435492713793854 0.2972737682473334 chr13 115169878 5494478 0.04770759590454719 0.25075318752570297 chr14 107349540 5297646 0.04934949884275238 0.38402367510038554 chr15 102531392 4839566 0.04720082216381106 0.2514167644572815 chr16 90354753 8907636 0.09858514028586852 0.436607263506303 chr17 81195210 5821286 0.07169494358103144 0.4926310596281195 chr18 78077248 7818958 0.10014387289879889 1.7244064515232707 chr19 59128983 4407042 0.07453268729482461 0.8454065824637362 chr20 63025520 4650058 0.0737805574630721 0.38170914750006935 chr21 48129895 5594206 0.11623141916266387 0.4327682190216835 chr22 51304566 3041100 0.05927542589484141 0.2837947409115146 chrMT 16571 2814 0.1698147365880152 0.4674435208521259 chrX 155270560 10127773 0.06522661475555959 0.4336544837752188 chrY 59373566 455390 0.007669911556263944 0.17083795031087134