BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093995.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 = 241,006 number of mapped reads = 230,052 (95.45%) number of supplementary alignments = 15,177 (6.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 115,728 number of mapped paired reads (second in pair) = 114,324 number of mapped paired reads (both in pair) = 227,722 number of mapped paired reads (singletons) = 2,330 number of mapped bases = 29,596,306 bp number of sequenced bases = 29,049,107 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 211,881 duplication rate = 49.97% >>>>>>> Insert size mean insert size = 1,179,549.8485 std insert size = 9,822,332.3211 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 40.541 >>>>>>> ACTG content number of A's = 7,772,650 bp (26.76%) number of C's = 6,791,228 bp (23.38%) number of T's = 7,325,510 bp (25.22%) number of G's = 7,159,394 bp (24.65%) number of N's = 325 bp (0%) GC percentage = 48.02% >>>>>>> Mismatches and indels general error rate = 0.0354 number of mismatches = 1,000,919 number of insertions = 14,569 mapped reads with insertion percentage = 6.23% number of deletions = 78,855 mapped reads with deletion percentage = 32.92% homopolymer indels = 29.41% >>>>>>> Coverage mean coverageData = 0.0096X std coverageData = 1.8788X There is a 0.01% 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 0.01% 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% 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 483147 0.0019383983801589005 0.6227222015349804 chr2 243199373 1694182 0.0069662268413825225 2.1005567076591025 chr3 198022430 486420 0.002456388400041349 0.8099440912921193 chr4 191154276 779849 0.004079683783793568 1.1421361002902817 chr5 180915260 404149 0.0022339132696711154 0.9686702722805866 chr6 171115067 524091 0.003062798672194074 0.915591033786707 chr7 159138663 484295 0.0030432265225201747 0.9747421200634416 chr8 146364022 369385 0.0025237417976939716 0.6674706777288957 chr9 141213431 499764 0.003539068461554482 1.1189028140378972 chr10 135534747 509311 0.003757789137275624 0.987174351465984 chr11 135006516 761944 0.005643757224280938 1.4478025002948753 chr12 133851895 738173 0.005514849080022363 1.377023600761278 chr13 115169878 543886 0.004722467449344698 1.346772820389671 chr14 107349540 108861 0.0010140797995035655 0.3934051126360845 chr15 102531392 462171 0.004507604851400047 1.206114895209199 chr16 90354753 271592 0.0030058407663402058 0.9756348388368465 chr17 81195210 679526 0.008369040488964804 1.9134049558092892 chr18 78077248 129111 0.001653631541931396 0.5035837501853198 chr19 59128983 134185 0.0022693608648739995 0.748212861648595 chr20 63025520 262200 0.0041602195428137685 1.411246686152335 chr21 48129895 83541 0.0017357403335286727 0.340697909041744 chr22 51304566 101686 0.0019820068256692787 0.5684174262527679 chrMT 16571 1268796 76.56725604972543 314.47948060572133 chrX 155270560 17301433 0.11142764603927492 5.744831367700498 chrY 59373566 514608 0.008667291434036486 1.7558108085038284