BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514746.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 3,300,983 number of mapped reads = 1,275,326 (38.63%) number of supplementary alignments = 329,658 (9.99%) number of secondary alignments = 0 number of mapped bases = 96,592,009 bp number of sequenced bases = 96,220,824 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,406,976 duplication rate = 23.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 30.947 >>>>>>> ACTG content number of A's = 26,935,838 bp (27.99%) number of C's = 19,604,036 bp (20.37%) number of T's = 27,074,121 bp (28.14%) number of G's = 22,601,539 bp (23.49%) number of N's = 5,290 bp (0.01%) GC percentage = 43.86% >>>>>>> Mismatches and indels general error rate = 0.0199 number of mismatches = 1,633,335 number of insertions = 91,703 mapped reads with insertion percentage = 6.6% number of deletions = 85,643 mapped reads with deletion percentage = 6.01% homopolymer indels = 24.43% >>>>>>> Coverage mean coverageData = 0.0312X std coverageData = 27.1608X There is a 0.21% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% 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% 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 3287749 0.013190534839229147 4.628960853262576 chr2 243199373 1314315 0.005404269689461741 3.3510465184691123 chr3 198022430 795854 0.004019009361717256 0.34107142087894043 chr4 191154276 1347754 0.0070506086926352615 4.999717731810043 chr5 180915260 946697 0.005232820050669026 0.3405019100827171 chr6 171115067 18575335 0.10855464294093985 60.78855058966247 chr7 159138663 1238623 0.00778329399437018 1.4449443004895448 chr8 146364022 716677 0.004896538030363774 0.5397686858940722 chr9 141213431 45003787 0.3186933897243811 105.78144974011444 chr10 135534747 805885 0.0059459660185885764 1.0720911468808074 chr11 135006516 1201312 0.008898177922019704 4.719882374844818 chr12 133851895 964765 0.007207705202828843 1.1832359187097727 chr13 115169878 1194678 0.010373181084727727 1.9658503007515207 chr14 107349540 755362 0.0070364716979690834 0.5373528558879729 chr15 102531392 291554 0.0028435583903903302 0.2788079470104035 chr16 90354753 1388381 0.015365887835474466 7.209885271786892 chr17 81195210 6857809 0.08446075821467794 22.088952075782323 chr18 78077248 438313 0.005613837721329522 0.5184091045292352 chr19 59128983 711198 0.012027908546981098 1.3898631218656348 chr20 63025520 863092 0.013694325727102292 1.418624110329037 chr21 48129895 360834 0.007497086789821586 0.7248029050966158 chr22 51304566 919425 0.017920919553242102 8.491861970043093 chrMT 16571 149475 9.02027638645827 12.628810836701145 chrX 155270560 3709408 0.023889963428997744 4.335159359888587 chrY 59373566 2753727 0.04637968014250651 7.030017909096961