BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094029.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 = 432,574 number of mapped reads = 402,472 (93.04%) number of supplementary alignments = 21,721 (5.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 202,344 number of mapped paired reads (second in pair) = 200,128 number of mapped paired reads (both in pair) = 396,912 number of mapped paired reads (singletons) = 5,560 number of mapped bases = 52,388,112 bp number of sequenced bases = 51,330,115 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 373,079 duplication rate = 44.61% >>>>>>> Insert size mean insert size = 485,335.1169 std insert size = 6,366,896.3927 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 44.8597 >>>>>>> ACTG content number of A's = 14,387,650 bp (28.03%) number of C's = 11,269,690 bp (21.96%) number of T's = 13,850,376 bp (26.98%) number of G's = 11,821,793 bp (23.03%) number of N's = 606 bp (0%) GC percentage = 44.99% >>>>>>> Mismatches and indels general error rate = 0.0372 number of mismatches = 1,839,461 number of insertions = 33,260 mapped reads with insertion percentage = 8.1% number of deletions = 130,937 mapped reads with deletion percentage = 31.32% homopolymer indels = 27.71% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 5.5724X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% 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 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 824969 0.003309797169973751 0.982434865729739 chr2 243199373 2622376 0.010782823852099322 2.5219987005096787 chr3 198022430 897339 0.004531501810173726 1.328975497468548 chr4 191154276 604287 0.0031612528510740717 0.6528074904553757 chr5 180915260 923445 0.005104295790194812 1.5916505383629884 chr6 171115067 1725844 0.01008586812521892 4.5495706372874745 chr7 159138663 1391719 0.008745322938901403 2.350553631275824 chr8 146364022 1074774 0.00734315704989304 2.2847072656131866 chr9 141213431 763931 0.0054097616252946935 1.9053332802906269 chr10 135534747 975418 0.007196811309206192 1.6870678900998388 chr11 135006516 1384054 0.010251757033712358 2.306147867875027 chr12 133851895 2259510 0.016880672477591743 5.016683229660518 chr13 115169878 719403 0.006246451003447273 1.8889100540848227 chr14 107349540 525277 0.004893146258474885 1.0499687186535516 chr15 102531392 543845 0.005304180401647137 1.3146136398283046 chr16 90354753 386626 0.0042789779968741655 1.011858439841194 chr17 81195210 1610842 0.019839125977997963 4.360589011663336 chr18 78077248 196163 0.0025124220566790467 0.5523802593407159 chr19 59128983 371238 0.006278443855528515 0.9145114221728383 chr20 63025520 552472 0.008765845962080122 3.0631406445162965 chr21 48129895 180137 0.0037427258048246316 0.5875631856623683 chr22 51304566 166226 0.0032399845269132574 0.43095000244197085 chrMT 16571 7440796 449.025164443908 1934.7957786942645 chrX 155270560 23856642 0.15364562348458072 9.768223150660214 chrY 59373566 390779 0.006581700011079004 1.0317985768620817