BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716395.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,964,153 number of mapped reads = 1,801,670 (91.73%) number of supplementary alignments = 28,333 (1.44%) number of secondary alignments = 0 number of mapped bases = 142,577,333 bp number of sequenced bases = 142,514,358 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,935 duplication rate = 2.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2009 >>>>>>> ACTG content number of A's = 35,678,478 bp (25.04%) number of C's = 27,832,363 bp (19.53%) number of T's = 44,351,749 bp (31.12%) number of G's = 34,642,959 bp (24.31%) number of N's = 8,809 bp (0.01%) GC percentage = 43.84% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,213,745 number of insertions = 13,146 mapped reads with insertion percentage = 0.72% number of deletions = 36,150 mapped reads with deletion percentage = 1.98% homopolymer indels = 43.78% >>>>>>> Coverage mean coverageData = 0.0461X std coverageData = 0.5295X There is a 3.92% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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% 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 10896196 0.04371582287853156 0.8162517286822512 chr2 243199373 12336639 0.05072644245674104 0.7717137599815018 chr3 198022430 9464352 0.04779434329737293 0.2485158901936742 chr4 191154276 9067115 0.04743349293426217 0.27373359823062515 chr5 180915260 8656673 0.04784932459539345 0.2561363905770695 chr6 171115067 9301587 0.05435866731712176 0.3306784918626709 chr7 159138663 7881853 0.04952820924478924 0.6893398663520938 chr8 146364022 6797722 0.046443940984349286 0.7220324238361765 chr9 141213431 6157732 0.0436058521940452 0.63240297753913 chr10 135534747 7440401 0.05489663104620692 0.4828654135451221 chr11 135006516 6501722 0.04815857924961192 0.571543147215696 chr12 133851895 6093962 0.04552764830113164 0.25214652588171127 chr13 115169878 4337194 0.03765910041165451 0.2166306912434659 chr14 107349540 4360458 0.04061925183843359 0.3331658100941815 chr15 102531392 3855012 0.03759835816917418 0.2222225767280914 chr16 90354753 3959875 0.043825862708074696 0.29343840206909905 chr17 81195210 4141298 0.05100421564277006 0.3171264197842697 chr18 78077248 3961069 0.05073269232030309 1.1957752949957705 chr19 59128983 2790065 0.047186081316500914 0.6087817186501905 chr20 63025520 2875566 0.0456254228445874 0.27729771870051323 chr21 48129895 2079922 0.0432147628828195 0.2586553991311564 chr22 51304566 1599009 0.03116699203731691 0.1998801309044383 chrMT 16571 23064 1.3918290990284232 1.579506149818934 chrX 155270560 7632280 0.04915471419694757 0.38533483168003085 chrY 59373566 366567 0.006173909109653276 0.17807178437406343