BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013176.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 = 2,097,768 number of mapped reads = 1,862,104 (88.77%) number of supplementary alignments = 13,759 (0.66%) number of secondary alignments = 0 number of mapped bases = 121,041,490 bp number of sequenced bases = 120,981,799 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,482 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0501 >>>>>>> ACTG content number of A's = 33,196,528 bp (27.44%) number of C's = 23,227,366 bp (19.2%) number of T's = 36,702,327 bp (30.34%) number of G's = 27,826,674 bp (23%) number of N's = 28,904 bp (0.02%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 994,704 number of insertions = 8,481 mapped reads with insertion percentage = 0.45% number of deletions = 34,067 mapped reads with deletion percentage = 1.81% homopolymer indels = 44.19% >>>>>>> Coverage mean coverageData = 0.0391X std coverageData = 0.3873X There is a 3.49% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 8965979 0.03597174187180861 0.7080180417468613 chr2 243199373 11433933 0.047014648347798164 0.4247989878627466 chr3 198022430 7683842 0.03880288712748349 0.21652576727088252 chr4 191154276 9164462 0.047942751748854415 0.25169725818426897 chr5 180915260 6775778 0.03745277208788247 0.2103751449967336 chr6 171115067 5770541 0.03372316126901905 0.24547665430804444 chr7 159138663 9391316 0.05901341523775401 0.7989231070870954 chr8 146364022 6183614 0.04224818309515982 0.35264586233974715 chr9 141213431 4058138 0.02873762057378239 0.29493942764463404 chr10 135534747 5334689 0.039360305147432044 0.40955915251087543 chr11 135006516 4857683 0.03598110034926018 0.2575798911899309 chr12 133851895 5925600 0.04426982524229485 0.23072597223155455 chr13 115169878 3126712 0.027148695946348056 0.17800355770681256 chr14 107349540 3572779 0.033281735534218405 0.23383899425741853 chr15 102531392 2816237 0.02746707076794588 0.17965178956089337 chr16 90354753 4043875 0.04475553156567204 0.26132442608117534 chr17 81195210 3633372 0.04474860031767884 0.2726562758533222 chr18 78077248 3090054 0.03957688160320405 0.5240352984004388 chr19 59128983 2462934 0.041653582981462746 0.5081394825426324 chr20 63025520 3003257 0.047651443415302246 0.24524617893350537 chr21 48129895 2281300 0.047398815227001845 0.25099322471358254 chr22 51304566 1139720 0.022214786886609664 0.15955249076100267 chrMT 16571 241503 14.573833806046709 9.542841979617473 chrX 155270560 5794053 0.03731585047416587 0.24122510828424687 chrY 59373566 290119 0.004886332749493268 0.12060357986867841