BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714216.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 157,346 number of mapped reads = 25,009 (15.89%) number of supplementary alignments = 631 (0.4%) number of secondary alignments = 0 number of mapped bases = 2,722,797 bp number of sequenced bases = 2,696,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,526 duplication rate = 38.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 28.2902 >>>>>>> ACTG content number of A's = 463,048 bp (17.17%) number of C's = 295,629 bp (10.96%) number of T's = 396,557 bp (14.71%) number of G's = 1,540,843 bp (57.15%) number of N's = 117 bp (0%) GC percentage = 68.11% >>>>>>> Mismatches and indels general error rate = 0.0366 number of mismatches = 84,295 number of insertions = 3,385 mapped reads with insertion percentage = 11.51% number of deletions = 4,687 mapped reads with deletion percentage = 18.1% homopolymer indels = 26.83% >>>>>>> Coverage mean coverageData = 0.0009X std coverageData = 1.7821X There is a 0% 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 58009 2.3273362275795493E-4 0.13343444089987513 chr2 243199373 1271790 0.005229413153133417 5.455405625179437 chr3 198022430 34775 1.756114193730478E-4 0.06582115207987178 chr4 191154276 31746 1.6607528047136126E-4 0.06217773276455297 chr5 180915260 46034 2.5445061958841945E-4 0.08148386274712356 chr6 171115067 49416 2.88788128750813E-4 0.08278141798418684 chr7 159138663 47695 2.9970718052344073E-4 0.0991468307065848 chr8 146364022 15380 1.0508046847742405E-4 0.04382407891621989 chr9 141213431 623149 0.00441281679502568 4.169680170219353 chr10 135534747 21895 1.6154528993218248E-4 0.05422996089302232 chr11 135006516 19852 1.470447544917017E-4 0.043985818487273745 chr12 133851895 25592 1.911963965844488E-4 0.06066104779745732 chr13 115169878 26761 2.3236110400325335E-4 0.0756710511248405 chr14 107349540 27007 2.515800254011335E-4 0.08322883328352652 chr15 102531392 14016 1.36699597329177E-4 0.037300158036073144 chr16 90354753 29598 3.275754624662634E-4 0.08413253454829568 chr17 81195210 17920 2.207026744557961E-4 0.06699225913885609 chr18 78077248 23374 2.9937018271955485E-4 0.08205290460343775 chr19 59128983 149138 0.002522248691475042 1.4170622150879253 chr20 63025520 20230 3.209810882956618E-4 0.07681250059429631 chr21 48129895 24216 5.031384340231783E-4 0.18898273654512984 chr22 51304566 4554 8.87640293068652E-5 0.02644182918963406 chrMT 16571 4912 0.2964214591756683 2.7635595247588913 chrX 155270560 129691 8.3525814552353E-4 0.14642604533655215 chrY 59373566 6047 1.0184667028421369E-4 0.05077074711011266