BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238065.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 = 2,187,258 number of mapped reads = 1,998,678 (91.38%) number of supplementary alignments = 10,237 (0.47%) number of secondary alignments = 0 number of mapped bases = 133,666,528 bp number of sequenced bases = 133,598,538 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,071 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1774 >>>>>>> ACTG content number of A's = 35,691,523 bp (26.72%) number of C's = 25,572,416 bp (19.14%) number of T's = 41,109,883 bp (30.77%) number of G's = 31,207,495 bp (23.36%) number of N's = 17,221 bp (0.01%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,034,936 number of insertions = 9,782 mapped reads with insertion percentage = 0.48% number of deletions = 38,252 mapped reads with deletion percentage = 1.89% homopolymer indels = 45.26% >>>>>>> Coverage mean coverageData = 0.0432X std coverageData = 0.439X There is a 3.76% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% 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 0.01% 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 10226660 0.04102962696329651 0.9354884054337892 chr2 243199373 12028002 0.04945737257307814 0.5888836958591139 chr3 198022430 10154277 0.05127841830847142 0.25321482347938457 chr4 191154276 7191248 0.03762012626910841 0.2460620663822863 chr5 180915260 5900008 0.032611997462237294 0.2045525358295305 chr6 171115067 7394223 0.04321199254768138 0.30058948008072744 chr7 159138663 4810304 0.030227123373532425 0.34318101662163575 chr8 146364022 9230283 0.0630638791820028 0.503044530657466 chr9 141213431 6405550 0.04536077025137927 0.43588531838462474 chr10 135534747 6750594 0.0498071096115301 0.41483766081041495 chr11 135006516 5520382 0.04088974490683102 0.34727527934409125 chr12 133851895 5894622 0.044038390341802784 0.23886206390169704 chr13 115169878 4005162 0.03477612436126745 0.2051977549312161 chr14 107349540 3350364 0.03120985893372249 0.2289840026923878 chr15 102531392 2366870 0.023084344743900483 0.17331397960352027 chr16 90354753 5093140 0.05636825768313483 0.30020735499757756 chr17 81195210 4645282 0.05721128130587999 0.29657485702022834 chr18 78077248 4295609 0.05501742325754105 0.7466994127036342 chr19 59128983 3270346 0.05530868000892219 0.5785879507559397 chr20 63025520 3787595 0.06009621182022774 0.28541436189943614 chr21 48129895 2379986 0.04944922485286951 0.2795314048578002 chr22 51304566 2039408 0.03975100383852775 0.22271840984484925 chrMT 16571 15245 0.919980689155754 1.1090243828379753 chrX 155270560 6558163 0.04223700230101572 0.2685919502494023 chrY 59373566 353205 0.005948859463822671 0.17470467874391385