BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818955.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 4,307,423 number of mapped reads = 4,022,563 (93.39%) number of supplementary alignments = 58,873 (1.37%) number of secondary alignments = 0 number of mapped bases = 372,459,922 bp number of sequenced bases = 372,251,161 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,251,873 duplication rate = 45.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1523 >>>>>>> ACTG content number of A's = 108,978,289 bp (29.28%) number of C's = 77,779,625 bp (20.89%) number of T's = 107,950,088 bp (29%) number of G's = 77,526,570 bp (20.83%) number of N's = 16,589 bp (0%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 2,393,405 number of insertions = 50,897 mapped reads with insertion percentage = 1.23% number of deletions = 115,042 mapped reads with deletion percentage = 2.8% homopolymer indels = 41.54% >>>>>>> Coverage mean coverageData = 0.1203X std coverageData = 1.2625X There is a 4.16% of reference with a coverageData >= 1X There is a 2.44% of reference with a coverageData >= 2X There is a 1.61% of reference with a coverageData >= 3X There is a 1.09% of reference with a coverageData >= 4X There is a 0.75% of reference with a coverageData >= 5X There is a 0.51% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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% 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 44232541 0.17746210951265795 2.222373867254919 chr2 243199373 32150859 0.1321995965836639 1.8752264055970822 chr3 198022430 25697740 0.1297718647326972 0.8153319938123478 chr4 191154276 24062156 0.12587819903123695 0.8939612765909349 chr5 180915260 19166769 0.10594335160008062 0.7574034093376465 chr6 171115067 19405298 0.11340496392407104 0.8188578890084589 chr7 159138663 18954715 0.11910817046389287 1.0488965922344895 chr8 146364022 24637800 0.16833235151190365 1.0997747884653066 chr9 141213431 13279911 0.09404141593302127 1.372569405300894 chr10 135534747 18616535 0.1373561792239152 1.5794194636993788 chr11 135006516 14210635 0.10525888246756919 0.9063127108982237 chr12 133851895 16210181 0.12110535304711226 0.7926796641116808 chr13 115169878 6236581 0.05415114705600366 0.5180187321218552 chr14 107349540 9561931 0.08907286421534737 0.7322902992379897 chr15 102531392 11197274 0.10920825106909697 0.7412143705441671 chr16 90354753 10630287 0.11765055680026042 1.3572670229452997 chr17 81195210 8164627 0.10055552538136178 0.7892371828103035 chr18 78077248 8864364 0.1135332536310706 1.631483764372428 chr19 59128983 5867558 0.09923319668799309 1.8708445187892784 chr20 63025520 7872680 0.12491257509656406 0.8528614761589793 chr21 48129895 4995699 0.10379617491374124 0.7797866760610696 chr22 51304566 4419161 0.08613582268681505 0.7143870075327677 chrMT 16571 972850 58.70798382716794 38.325232872307915 chrX 155270560 21986177 0.14159913508394636 1.0253783203500484 chrY 59373566 1065593 0.017947262928421717 1.0763901360093178