BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081168.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 = 2,684,261 number of mapped reads = 2,358,686 (87.87%) number of supplementary alignments = 20,707 (0.77%) number of secondary alignments = 0 number of mapped bases = 157,676,134 bp number of sequenced bases = 157,620,860 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,322 duplication rate = 3.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.542 >>>>>>> ACTG content number of A's = 43,823,308 bp (27.8%) number of C's = 29,197,129 bp (18.52%) number of T's = 49,555,698 bp (31.44%) number of G's = 34,997,733 bp (22.2%) number of N's = 46,992 bp (0.03%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,315,548 number of insertions = 12,131 mapped reads with insertion percentage = 0.51% number of deletions = 34,631 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.01% >>>>>>> Coverage mean coverageData = 0.0509X std coverageData = 0.4205X There is a 4.34% of reference with a coverageData >= 1X There is a 0.56% 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 13127102 0.05266627600498536 0.770806533611051 chr2 243199373 12541598 0.05156920367553744 0.48801140530539683 chr3 198022430 10061977 0.05081230949443454 0.2549252247488798 chr4 191154276 10238656 0.05356226506803332 0.2718535112977195 chr5 180915260 8613137 0.04760868154516098 0.2502552657651942 chr6 171115067 9192898 0.05372348654721328 0.31772523225200083 chr7 159138663 7926772 0.04981047251854818 0.6137414425417896 chr8 146364022 6918739 0.047270763029455425 0.4575264562746611 chr9 141213431 6734960 0.04769348037439866 0.39593026509524365 chr10 135534747 7392537 0.05454348175379706 0.3591960408455509 chr11 135006516 8425294 0.062406573027927036 0.4284934758203281 chr12 133851895 6859481 0.05124679781335931 0.26128646134331235 chr13 115169878 5689708 0.049402744005685235 0.25155773964541767 chr14 107349540 5007300 0.04664482027589499 0.2611116505282878 chr15 102531392 4335722 0.042286775936876 0.2388769403545763 chr16 90354753 4833031 0.05348950486312546 0.29191674447263016 chr17 81195210 4148958 0.051098556183301946 0.30784049957628257 chr18 78077248 4404589 0.056413220404489664 0.6967318969755616 chr19 59128983 3190070 0.053951037852283036 0.5707359259172435 chr20 63025520 3376645 0.05357583721641646 0.267811867513501 chr21 48129895 2178058 0.04525374509958935 0.25935820490131 chr22 51304566 1642324 0.03201126387074398 0.20063829249209278 chrMT 16571 13690 0.8261420553979845 1.0818703876547406 chrX 155270560 10431002 0.06717952199051772 0.33600791652987916 chrY 59373566 391886 0.006600344671903318 0.12917605174152416