BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237277.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 = 2,466,311 number of mapped reads = 2,239,762 (90.81%) number of supplementary alignments = 10,480 (0.42%) number of secondary alignments = 0 number of mapped bases = 152,409,524 bp number of sequenced bases = 152,346,688 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,660 duplication rate = 2.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9354 >>>>>>> ACTG content number of A's = 42,767,697 bp (28.07%) number of C's = 28,529,733 bp (18.73%) number of T's = 47,301,734 bp (31.05%) number of G's = 33,744,992 bp (22.15%) number of N's = 2,532 bp (0%) GC percentage = 40.88% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,172,201 number of insertions = 12,182 mapped reads with insertion percentage = 0.54% number of deletions = 35,605 mapped reads with deletion percentage = 1.57% homopolymer indels = 47.81% >>>>>>> Coverage mean coverageData = 0.0492X std coverageData = 0.5458X There is a 4.17% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 12950839 0.05195910424632402 1.2118477626122 chr2 243199373 12921299 0.053130478259909 0.5768473951527433 chr3 198022430 12618891 0.06372455382958385 0.2932923071122429 chr4 191154276 8466716 0.044292579675277576 0.2627329735391998 chr5 180915260 7358211 0.040672141200250325 0.23724977250341076 chr6 171115067 9903873 0.0578784391908633 0.3700992263422005 chr7 159138663 7876314 0.04949340312102534 0.5707057026948507 chr8 146364022 7486188 0.05114773355982251 0.6765349368665022 chr9 141213431 6503870 0.04605702130415626 0.5260845831040805 chr10 135534747 6937745 0.05118794370863436 0.5085606138475315 chr11 135006516 5578675 0.04132152406629025 0.3566853184211924 chr12 133851895 6507253 0.048615322181281034 0.26393758490673075 chr13 115169878 3170872 0.027532129538246103 0.18572261423281972 chr14 107349540 5206241 0.04849802803067437 0.2954552674378152 chr15 102531392 3970737 0.03872703688642011 0.23074104812163365 chr16 90354753 4533644 0.050176043312298135 0.32508803713312 chr17 81195210 6003513 0.0739392508498962 0.4628926459620516 chr18 78077248 4403934 0.05640483127684009 1.0572212065038527 chr19 59128983 4575051 0.07737408573389466 0.7332037723684917 chr20 63025520 3300601 0.0523692783494686 0.2750565506921774 chr21 48129895 2284335 0.04746187374811435 0.28830706906361514 chr22 51304566 1190870 0.023211774172302715 0.1686500251334513 chrMT 16571 37694 2.27469675939895 2.017430921826214 chrX 155270560 8232022 0.05301727513573726 0.30932007089625296 chrY 59373566 390136 0.0065708702758395885 0.1621290404205403