BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082907.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,907,499 number of mapped reads = 1,692,297 (88.72%) number of supplementary alignments = 21,079 (1.11%) number of secondary alignments = 0 number of mapped bases = 112,273,005 bp number of sequenced bases = 112,231,992 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,437 duplication rate = 4.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.051 >>>>>>> ACTG content number of A's = 30,476,238 bp (27.15%) number of C's = 21,145,534 bp (18.84%) number of T's = 35,175,185 bp (31.34%) number of G's = 25,430,119 bp (22.66%) number of N's = 4,916 bp (0%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 806,559 number of insertions = 8,766 mapped reads with insertion percentage = 0.51% number of deletions = 25,056 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.77% >>>>>>> Coverage mean coverageData = 0.0363X std coverageData = 0.2895X There is a 2.99% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.09% 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% of reference with a coverageData >= 6X There is a 0% 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 11294979 0.04531575068773851 0.47476652690164173 chr2 243199373 9775475 0.04019531333248955 0.43101223644963427 chr3 198022430 9065740 0.04578137941242313 0.25062543638532053 chr4 191154276 5536182 0.028961852781153586 0.20054166280401411 chr5 180915260 5234392 0.028932838501296132 0.20073359215858097 chr6 171115067 6258511 0.03657486806816375 0.2553895140049708 chr7 159138663 5419405 0.03405460934405362 0.23729262665808537 chr8 146364022 9824868 0.06712625046611523 0.34442959679972707 chr9 141213431 3259740 0.023083781598649777 0.22297797909576036 chr10 135534747 4367692 0.03222562550694104 0.23043929693223314 chr11 135006516 4697854 0.03479723897178415 0.2466946904030519 chr12 133851895 3274128 0.02446082664724321 0.18517656873805788 chr13 115169878 2195847 0.019066157211697316 0.1646026216194256 chr14 107349540 2637001 0.024564623192609863 0.19062799707647113 chr15 102531392 2627306 0.0256244058405059 0.18879097084767738 chr16 90354753 5313339 0.05880530712092146 0.29754985432672554 chr17 81195210 3345252 0.04120011512994424 0.24877625043207244 chr18 78077248 3822053 0.04895219923735017 0.42956431191446126 chr19 59128983 2363987 0.03998017351321601 0.3435048840691498 chr20 63025520 2230314 0.03538747478799064 0.22687148685830222 chr21 48129895 2635970 0.054767831926498076 0.28031979973560595 chr22 51304566 1835633 0.035779135135847365 0.22338658636387912 chrMT 16571 207048 12.494598998249955 7.650358960854236 chrX 155270560 4852889 0.031254405213712116 0.21666066480660903 chrY 59373566 197400 0.003324711875988719 0.07089572756708377