BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085025.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 = 2,613,553 number of mapped reads = 2,336,128 (89.39%) number of supplementary alignments = 15,476 (0.59%) number of secondary alignments = 0 number of mapped bases = 155,950,155 bp number of sequenced bases = 155,890,939 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,611 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9014 >>>>>>> ACTG content number of A's = 43,210,483 bp (27.72%) number of C's = 30,149,531 bp (19.34%) number of T's = 47,365,664 bp (30.38%) number of G's = 35,157,744 bp (22.55%) number of N's = 7,517 bp (0%) GC percentage = 41.89% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,397,247 number of insertions = 11,588 mapped reads with insertion percentage = 0.49% number of deletions = 34,670 mapped reads with deletion percentage = 1.47% homopolymer indels = 45.35% >>>>>>> Coverage mean coverageData = 0.0504X std coverageData = 0.4612X There is a 4.33% of reference with a coverageData >= 1X There is a 0.5% 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% 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 13550064 0.05436321059356558 0.7533098936426365 chr2 243199373 15640375 0.06431091826869142 0.6266826574867697 chr3 198022430 8833013 0.04460612365982985 0.2515936972848624 chr4 191154276 8969435 0.046922492071273365 0.253166218576026 chr5 180915260 7464447 0.041259355346807115 0.2289649511474029 chr6 171115067 11272804 0.0658785003426963 0.4395687944175016 chr7 159138663 13926562 0.0875121214258285 0.5855395547974072 chr8 146364022 8721355 0.05958674051742033 0.7428668298678853 chr9 141213431 5175751 0.036651973989641255 0.4469789611503906 chr10 135534747 11752847 0.08671464152288565 0.5919467554400029 chr11 135006516 6078358 0.04502270097837352 0.39101241582473645 chr12 133851895 5352147 0.039985590043383396 0.23643856938450783 chr13 115169878 3285409 0.028526634368753957 0.18799175306265947 chr14 107349540 5475391 0.05100525815015137 0.27636387273379315 chr15 102531392 2848084 0.02777767807931448 0.19984495331308297 chr16 90354753 4502556 0.04983197729509592 0.2782926200179739 chr17 81195210 2670576 0.03289080722865302 0.24064124760387962 chr18 78077248 4029579 0.05161015664896386 0.7798514011704197 chr19 59128983 2686248 0.045430309531959985 0.5072374367973114 chr20 63025520 3599516 0.05711203969439681 0.27503484416908486 chr21 48129895 1823636 0.037889881122740866 0.23719731710787312 chr22 51304566 1179892 0.02299779711614752 0.1669191144934846 chrMT 16571 7938 0.4790296300766399 0.7481548084065615 chrX 155270560 6776791 0.043645047715420104 0.29613675730483946 chrY 59373566 327381 0.005513918432994238 0.11349837823719466