BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238604.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 = 3,172,059 number of mapped reads = 2,789,837 (87.95%) number of supplementary alignments = 25,298 (0.8%) number of secondary alignments = 0 number of mapped bases = 169,643,876 bp number of sequenced bases = 169,550,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,284,985 duplication rate = 23.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.2828 >>>>>>> ACTG content number of A's = 42,269,715 bp (24.93%) number of C's = 28,791,267 bp (16.98%) number of T's = 58,283,018 bp (34.37%) number of G's = 40,202,914 bp (23.71%) number of N's = 3,909 bp (0%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,105,959 number of insertions = 16,015 mapped reads with insertion percentage = 0.57% number of deletions = 52,872 mapped reads with deletion percentage = 1.87% homopolymer indels = 42.21% >>>>>>> Coverage mean coverageData = 0.0548X std coverageData = 1.1299X There is a 1.24% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 9531002 0.03823862890195166 1.6075155850597138 chr2 243199373 8977581 0.03691449072938194 1.9419938117271385 chr3 198022430 4198412 0.02120169922164878 0.4560801834010087 chr4 191154276 25094630 0.13127945932007296 1.3421289132685323 chr5 180915260 5332357 0.029474335111366504 0.5338985605915227 chr6 171115067 4177898 0.024415722550019513 0.7078701211225993 chr7 159138663 11192103 0.07032925116381052 0.949822465099103 chr8 146364022 4373884 0.029883600766314005 1.0104006821654017 chr9 141213431 20694854 0.1465501819016068 1.258919516019102 chr10 135534747 4835087 0.035674150776995955 1.2639394405417166 chr11 135006516 11792544 0.08734796178282239 1.0012759117741956 chr12 133851895 5834025 0.04358567355359444 0.6638604205701415 chr13 115169878 3716581 0.03227042577921286 0.6948299600833417 chr14 107349540 10371653 0.09661571907993272 1.0272957342984042 chr15 102531392 1972396 0.019236996216729408 0.5414171795305432 chr16 90354753 7191012 0.07958642751200924 0.9372495072859406 chr17 81195210 7411593 0.09128116055121971 1.0671885472727405 chr18 78077248 6894861 0.08830819703071502 2.0456340247066516 chr19 59128983 2647888 0.04478155830956876 0.9989768048419845 chr20 63025520 1007344 0.01598311287237297 0.45614050698951325 chr21 48129895 1760241 0.036572716395911524 0.79542182651863 chr22 51304566 4455547 0.08684503831491333 0.9434770801777643 chrMT 16571 5822 0.3513366725001509 1.4527024646187252 chrX 155270560 5425751 0.03494384898206073 0.6122110006788783 chrY 59373566 748810 0.012611841437989425 0.7339241666395847