BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514740.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 38,206,159 number of mapped reads = 37,340,282 (97.73%) number of supplementary alignments = 1,257,316 (3.29%) number of secondary alignments = 0 number of mapped bases = 3,575,805,564 bp number of sequenced bases = 3,573,334,159 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,630,071 duplication rate = 34.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7087 >>>>>>> ACTG content number of A's = 935,856,985 bp (26.19%) number of C's = 844,043,494 bp (23.62%) number of T's = 946,500,793 bp (26.49%) number of G's = 846,780,314 bp (23.7%) number of N's = 152,573 bp (0%) GC percentage = 47.32% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 29,471,571 number of insertions = 1,258,075 mapped reads with insertion percentage = 3.26% number of deletions = 1,083,999 mapped reads with deletion percentage = 2.77% homopolymer indels = 40.25% >>>>>>> Coverage mean coverageData = 1.1551X std coverageData = 50.1186X There is a 7.58% of reference with a coverageData >= 1X There is a 4.27% of reference with a coverageData >= 2X There is a 3.07% of reference with a coverageData >= 3X There is a 2.51% of reference with a coverageData >= 4X There is a 2.17% of reference with a coverageData >= 5X There is a 1.94% of reference with a coverageData >= 6X There is a 1.78% of reference with a coverageData >= 7X There is a 1.65% of reference with a coverageData >= 8X There is a 1.54% of reference with a coverageData >= 9X There is a 1.45% of reference with a coverageData >= 10X There is a 1.37% of reference with a coverageData >= 11X There is a 1.31% of reference with a coverageData >= 12X There is a 1.25% of reference with a coverageData >= 13X There is a 1.19% of reference with a coverageData >= 14X There is a 1.15% of reference with a coverageData >= 15X There is a 1.1% of reference with a coverageData >= 16X There is a 1.06% of reference with a coverageData >= 17X There is a 1.02% of reference with a coverageData >= 18X There is a 0.99% of reference with a coverageData >= 19X There is a 0.96% of reference with a coverageData >= 20X There is a 0.93% of reference with a coverageData >= 21X There is a 0.9% of reference with a coverageData >= 22X There is a 0.87% of reference with a coverageData >= 23X There is a 0.85% of reference with a coverageData >= 24X There is a 0.82% of reference with a coverageData >= 25X There is a 0.8% of reference with a coverageData >= 26X There is a 0.78% of reference with a coverageData >= 27X There is a 0.76% of reference with a coverageData >= 28X There is a 0.74% of reference with a coverageData >= 29X There is a 0.72% of reference with a coverageData >= 30X There is a 0.7% of reference with a coverageData >= 31X There is a 0.69% of reference with a coverageData >= 32X There is a 0.67% of reference with a coverageData >= 33X There is a 0.66% of reference with a coverageData >= 34X There is a 0.64% of reference with a coverageData >= 35X There is a 0.63% of reference with a coverageData >= 36X There is a 0.61% of reference with a coverageData >= 37X There is a 0.6% of reference with a coverageData >= 38X There is a 0.59% of reference with a coverageData >= 39X There is a 0.57% of reference with a coverageData >= 40X There is a 0.56% of reference with a coverageData >= 41X There is a 0.55% of reference with a coverageData >= 42X There is a 0.54% of reference with a coverageData >= 43X There is a 0.53% of reference with a coverageData >= 44X There is a 0.52% of reference with a coverageData >= 45X There is a 0.51% of reference with a coverageData >= 46X There is a 0.5% of reference with a coverageData >= 47X There is a 0.49% of reference with a coverageData >= 48X There is a 0.48% of reference with a coverageData >= 49X There is a 0.47% of reference with a coverageData >= 50X There is a 0.46% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 458685689 1.8402589616817846 17.745266210395908 chr2 243199373 399932116 1.6444619534442633 150.1356786845927 chr3 198022430 216472397 1.0931710968297885 15.119270216436894 chr4 191154276 204257375 1.068547245053519 14.259933461446218 chr5 180915260 127043906 0.7022288003786966 13.418680707587754 chr6 171115067 54124801 0.31630645944228863 6.994436115211826 chr7 159138663 144391867 0.9073336691285385 58.70990102630757 chr8 146364022 173697269 1.186748400505146 25.345093125966375 chr9 141213431 136574395 0.9671487622165345 23.89719288461592 chr10 135534747 211089405 1.557456000563457 24.993646212597476 chr11 135006516 230997743 1.7110118077560048 34.80323798205488 chr12 133851895 166921018 1.2470575631372272 12.915137649329651 chr13 115169878 87962270 0.7637610764856415 9.486741424265936 chr14 107349540 72306265 0.6735591507890951 10.52273546283476 chr15 102531392 22662542 0.22103027724426097 3.0064847156774124 chr16 90354753 122652462 1.3574544551076355 42.799013795306855 chr17 81195210 269212227 3.3156171035212547 96.72874258768672 chr18 78077248 36016900 0.46129827731633166 9.600020942344209 chr19 59128983 314924180 5.32605439873708 45.50066105135545 chr20 63025520 29007168 0.46024480242289156 6.221030555838712 chr21 48129895 6680096 0.13879307237217117 3.329479853961056 chr22 51304566 51527780 1.0043507628541288 11.984419886641572 chrMT 16571 5019409 302.90320439321704 123.12915193215193 chrX 155270560 19981151 0.1286860239313879 3.1173463319491135 chrY 59373566 13665133 0.23015516703173935 7.023747224513949