BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084363.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 = 2,408,283 number of mapped reads = 2,169,854 (90.1%) number of supplementary alignments = 12,665 (0.53%) number of secondary alignments = 0 number of mapped bases = 145,450,475 bp number of sequenced bases = 145,401,913 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,678 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8513 >>>>>>> ACTG content number of A's = 40,070,695 bp (27.56%) number of C's = 27,949,284 bp (19.22%) number of T's = 44,787,320 bp (30.8%) number of G's = 32,405,758 bp (22.29%) number of N's = 188,856 bp (0.13%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 1,446,342 number of insertions = 9,868 mapped reads with insertion percentage = 0.45% number of deletions = 27,930 mapped reads with deletion percentage = 1.27% homopolymer indels = 46.69% >>>>>>> Coverage mean coverageData = 0.047X std coverageData = 0.3233X There is a 3.98% of reference with a coverageData >= 1X There is a 0.54% 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 14354930 0.05759235400260046 0.5218689053384139 chr2 243199373 12897564 0.05303288343592892 0.36794616896216614 chr3 198022430 9682195 0.04889443584749465 0.25447633331241687 chr4 191154276 6859254 0.03588334063738129 0.2214382611044869 chr5 180915260 7463841 0.04125600571228762 0.23166133812423473 chr6 171115067 7231714 0.04226228658169535 0.26096577568345075 chr7 159138663 8082163 0.05078692284853493 0.4478136151852921 chr8 146364022 7111582 0.04858832042754332 0.2958235457217057 chr9 141213431 5283608 0.03741576111127843 0.27442035692133915 chr10 135534747 10277426 0.07582871719235215 0.4368102563762685 chr11 135006516 8273319 0.0612808866203169 0.3364628720141018 chr12 133851895 7402131 0.055300905526963214 0.26880976470566437 chr13 115169878 3471971 0.03014651973496056 0.19769412948234058 chr14 107349540 3842861 0.03579764757259323 0.22444765738559677 chr15 102531392 3321734 0.032397238886603626 0.20756456996364026 chr16 90354753 3589527 0.03972704125481921 0.24092812396862975 chr17 81195210 4152909 0.051147216689260366 0.2718371838256689 chr18 78077248 3928675 0.050317795524760296 0.4369739675777059 chr19 59128983 3132391 0.05297556022568492 0.40007657875465474 chr20 63025520 3003837 0.047660646036716554 0.25167781153500385 chr21 48129895 1466578 0.03047124869065266 0.20662783866901266 chr22 51304566 1164111 0.022690202661494106 0.16926192647193963 chrMT 16571 57170 3.4500030173194136 2.5920833542739965 chrX 155270560 9107832 0.058657816394814315 0.3029917565257545 chrY 59373566 291152 0.004903731064426886 0.09963253470865813