BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237318.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 = 2,285,381 number of mapped reads = 2,090,917 (91.49%) number of supplementary alignments = 14,054 (0.61%) number of secondary alignments = 0 number of mapped bases = 142,814,006 bp number of sequenced bases = 142,745,092 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,917 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4404 >>>>>>> ACTG content number of A's = 40,737,675 bp (28.54%) number of C's = 26,861,195 bp (18.82%) number of T's = 44,156,850 bp (30.93%) number of G's = 30,987,173 bp (21.71%) number of N's = 2,199 bp (0%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,143,811 number of insertions = 11,524 mapped reads with insertion percentage = 0.55% number of deletions = 39,737 mapped reads with deletion percentage = 1.88% homopolymer indels = 46.94% >>>>>>> Coverage mean coverageData = 0.0461X std coverageData = 0.4548X There is a 4% of reference with a coverageData >= 1X There is a 0.43% 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% 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 11888449 0.047696767824702835 0.7170038058473831 chr2 243199373 11096861 0.04562865793243636 0.4830116286975267 chr3 198022430 11040665 0.0557546183025832 0.2614174095787735 chr4 191154276 5859903 0.03065535923454833 0.23078521574429856 chr5 180915260 8749865 0.04836443868803549 0.24904240502159947 chr6 171115067 11185550 0.06536858615729028 0.4354638746056352 chr7 159138663 10297550 0.06470803389871385 0.80551720049186 chr8 146364022 10260334 0.07010147616741497 0.6816503759691349 chr9 141213431 6671885 0.04724681606241831 0.4788838739464253 chr10 135534747 6674906 0.04924866978945259 0.38983957293777166 chr11 135006516 3199431 0.023698345048767867 0.29705698907225414 chr12 133851895 4680829 0.03497021091856787 0.22118058567342938 chr13 115169878 4666134 0.04051522916434799 0.22273561375784373 chr14 107349540 6856075 0.06386683166038717 0.31912597711960533 chr15 102531392 4999123 0.04875699922224795 0.2509808505667645 chr16 90354753 3536833 0.03914385112645928 0.290721606985696 chr17 81195210 2977635 0.036672545092253594 0.25632470730591367 chr18 78077248 3957874 0.050691771308333 0.9736100164066033 chr19 59128983 1924547 0.03254828516161017 0.4841644677210486 chr20 63025520 2618866 0.041552469539323116 0.23590934531953814 chr21 48129895 2126463 0.04418175024067682 0.2807255109987707 chr22 51304566 1358201 0.026473296743217748 0.17760836543201486 chrMT 16571 18771 1.1327620541910566 1.2571389803356863 chrX 155270560 5846375 0.03765282356165908 0.25514588772012503 chrY 59373566 320881 0.005404442104757528 0.17413846410264144