BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094077.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 = 431,474 number of mapped reads = 419,905 (97.32%) number of supplementary alignments = 14,913 (3.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 211,068 number of mapped paired reads (second in pair) = 208,837 number of mapped paired reads (both in pair) = 416,930 number of mapped paired reads (singletons) = 2,975 number of mapped bases = 56,508,154 bp number of sequenced bases = 55,334,105 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 401,203 duplication rate = 49.68% >>>>>>> Insert size mean insert size = 469,009.5485 std insert size = 6,199,017.5792 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 38.3974 >>>>>>> ACTG content number of A's = 14,567,064 bp (26.33%) number of C's = 13,055,690 bp (23.59%) number of T's = 13,984,109 bp (25.27%) number of G's = 13,726,650 bp (24.81%) number of N's = 592 bp (0%) GC percentage = 48.4% >>>>>>> Mismatches and indels general error rate = 0.0395 number of mismatches = 2,106,035 number of insertions = 34,224 mapped reads with insertion percentage = 8.05% number of deletions = 166,408 mapped reads with deletion percentage = 37.85% homopolymer indels = 29.25% >>>>>>> Coverage mean coverageData = 0.0183X std coverageData = 4.9485X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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% 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 359131 0.001440842949795499 0.571617926926962 chr2 243199373 2783224 0.01144420713617547 5.0188862153406495 chr3 198022430 800726 0.004043612635194912 1.2605602979194743 chr4 191154276 897810 0.00469678219492197 1.6467111469788345 chr5 180915260 322762 0.0017840507207628588 0.9289453622970963 chr6 171115067 1235274 0.007218966872157435 4.301894652662176 chr7 159138663 1617039 0.010161195083057848 3.7716888418172365 chr8 146364022 1201523 0.008209141724733419 2.792572091197272 chr9 141213431 496977 0.0035193323785185845 1.207036050349939 chr10 135534747 1145328 0.008450438174352442 3.1796920433903155 chr11 135006516 1516388 0.01123196157435838 3.2331280277266226 chr12 133851895 1747677 0.01305679684251015 4.570987737737193 chr13 115169878 1379008 0.011973686383517746 3.7415027786121797 chr14 107349540 262297 0.0024433919325597482 1.2018472356011023 chr15 102531392 792284 0.007727233431103715 2.606554644502644 chr16 90354753 335768 0.003716107773544575 1.2244474206365865 chr17 81195210 886205 0.010914498527684084 4.0399077415339555 chr18 78077248 110670 0.0014174423770673885 0.45578847877328277 chr19 59128983 230265 0.0038942831132407606 0.9614205158963581 chr20 63025520 335867 0.005329063528551609 2.007869123024392 chr21 48129895 872468 0.018127361383190217 8.01024991817117 chr22 51304566 44402 8.654590314632035E-4 0.2470727984586275 chrMT 16571 1773089 106.99951722889385 496.76053535469595 chrX 155270560 34825175 0.224287044498326 16.88192810430792 chrY 59373566 536797 0.009041009933612544 2.5114968142109118