BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093983.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 489,974 number of mapped reads = 481,983 (98.37%) number of supplementary alignments = 29,134 (5.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 242,504 number of mapped paired reads (second in pair) = 239,479 number of mapped paired reads (both in pair) = 477,774 number of mapped paired reads (singletons) = 4,209 number of mapped bases = 64,652,230 bp number of sequenced bases = 64,112,963 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 497,875 duplication rate = 47.36% >>>>>>> Insert size mean insert size = 430,867.9282 std insert size = 5,347,853.2534 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 19.0751 >>>>>>> ACTG content number of A's = 17,998,580 bp (28.07%) number of C's = 13,618,530 bp (21.24%) number of T's = 17,077,727 bp (26.64%) number of G's = 15,417,387 bp (24.05%) number of N's = 739 bp (0%) GC percentage = 45.29% >>>>>>> Mismatches and indels general error rate = 0.0263 number of mismatches = 1,610,668 number of insertions = 32,899 mapped reads with insertion percentage = 6.74% number of deletions = 127,168 mapped reads with deletion percentage = 25.63% homopolymer indels = 33.52% >>>>>>> Coverage mean coverageData = 0.0209X std coverageData = 14.1549X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 1282487 0.005145371332896298 4.938564073866889 chr2 243199373 2887743 0.01187397386916783 12.394892093129059 chr3 198022430 5074621 0.025626495947959026 14.996627131973899 chr4 191154276 2185395 0.011432624190944074 8.217502754230404 chr5 180915260 165452 9.145276081188508E-4 0.6621276490515301 chr6 171115067 1214592 0.007098100835270105 6.8815993191634375 chr7 159138663 316152 0.001986644816791002 1.2986356286051548 chr8 146364022 1661526 0.011352011083707442 6.49650613204445 chr9 141213431 16914 1.1977614225661014E-4 0.02318599533883401 chr10 135534747 328419 0.002423135079892096 1.1426421612831663 chr11 135006516 599513 0.00444062270298124 2.8625551312969626 chr12 133851895 663301 0.004955484567476613 3.9017975092856965 chr13 115169878 307603 0.0026708632963907456 2.3013959024181063 chr14 107349540 27003 2.5154276394663636E-4 0.12765721452510734 chr15 102531392 115260 0.001124143520844816 0.6738018643416614 chr16 90354753 196457 0.0021742851756785834 0.8987504533464858 chr17 81195210 22242 2.739324154713067E-4 0.1323823422656224 chr18 78077248 10255 1.3134428098695282E-4 0.04383246659887215 chr19 59128983 186099 0.003147339774134116 1.2298514067339188 chr20 63025520 271245 0.004303732837111062 2.182110034383287 chr21 48129895 14792 3.0733497340893845E-4 0.12686220865607217 chr22 51304566 12295 2.3964728597450762E-4 0.08039844112621843 chrMT 16571 7603078 458.8182970249231 2453.0006593398543 chrX 155270560 39222442 0.2526070750308365 50.53977523139224 chrY 59373566 267344 0.00450274453786387 2.8956690619582357