BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094057.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 = 424,800 number of mapped reads = 406,058 (95.59%) number of supplementary alignments = 17,338 (4.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 203,957 number of mapped paired reads (second in pair) = 202,101 number of mapped paired reads (both in pair) = 403,004 number of mapped paired reads (singletons) = 3,054 number of mapped bases = 53,551,524 bp number of sequenced bases = 52,160,753 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 381,430 duplication rate = 50.05% >>>>>>> Insert size mean insert size = 649,875.0916 std insert size = 7,174,792.3896 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 44.0246 >>>>>>> ACTG content number of A's = 14,588,115 bp (27.97%) number of C's = 11,627,913 bp (22.29%) number of T's = 13,895,505 bp (26.64%) number of G's = 12,048,622 bp (23.1%) number of N's = 598 bp (0%) GC percentage = 45.39% >>>>>>> Mismatches and indels general error rate = 0.0457 number of mismatches = 2,304,511 number of insertions = 39,132 mapped reads with insertion percentage = 9.45% number of deletions = 185,126 mapped reads with deletion percentage = 42.37% homopolymer indels = 27.95% >>>>>>> Coverage mean coverageData = 0.0173X std coverageData = 3.786X 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 0.01% 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% 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 1186910 0.004761913913145276 1.8427973221923273 chr2 243199373 2202045 0.009054484692277558 2.6889724393548677 chr3 198022430 1370468 0.006920771550980361 1.8387018907686874 chr4 191154276 1467708 0.007678133237260149 2.6865173236002327 chr5 180915260 549342 0.003036460274274265 1.2611487649547173 chr6 171115067 1567109 0.009158217493495182 3.799600731437103 chr7 159138663 1494052 0.009388365918343803 2.5483568548169253 chr8 146364022 730061 0.004987981267691592 1.3559514038115608 chr9 141213431 581845 0.004120323370657286 1.2609183564916686 chr10 135534747 1365765 0.010076862429971556 3.1816384678450733 chr11 135006516 2039531 0.015106907876950177 3.7508986142779728 chr12 133851895 1698369 0.012688419540119324 3.249853646833711 chr13 115169878 1537806 0.0133525017713399 3.3091989502005896 chr14 107349540 334732 0.003118150296685016 1.235844925106689 chr15 102531392 712077 0.006944965694018862 2.0220168846577993 chr16 90354753 537438 0.005948087755826194 2.245651875091362 chr17 81195210 1388410 0.017099654031315394 4.269571534594093 chr18 78077248 170881 0.0021886145372336896 0.6326910076729528 chr19 59128983 224586 0.003798238843377367 0.9462616896450674 chr20 63025520 196319 0.0031149128162687115 0.7203073986969089 chr21 48129895 223495 0.004643579629666759 1.123312333989874 chr22 51304566 90234 0.0017587908257522343 0.3605315074465335 chrMT 16571 2547941 153.75903687164322 639.8161768142704 chrX 155270560 28876182 0.18597332295317284 11.172306275374643 chrY 59373566 458218 0.007717542180302931 1.942131381681901