BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080680.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 = 1,377,245 number of mapped reads = 1,273,328 (92.45%) number of supplementary alignments = 10,283 (0.75%) number of secondary alignments = 0 number of mapped bases = 85,224,703 bp number of sequenced bases = 85,191,871 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,765 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1291 >>>>>>> ACTG content number of A's = 23,576,990 bp (27.68%) number of C's = 15,512,501 bp (18.21%) number of T's = 27,219,917 bp (31.95%) number of G's = 18,878,798 bp (22.16%) number of N's = 3,665 bp (0%) GC percentage = 40.37% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 579,613 number of insertions = 6,255 mapped reads with insertion percentage = 0.49% number of deletions = 20,149 mapped reads with deletion percentage = 1.57% homopolymer indels = 48.83% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 0.231X There is a 2.42% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 10545963 0.042310678937084775 0.2520384187328715 chr2 243199373 5683378 0.02336921320927912 0.28457470117223665 chr3 198022430 5282587 0.02667671031003912 0.18054496071748746 chr4 191154276 3759440 0.01966704631812683 0.15842369020021063 chr5 180915260 3881108 0.021452629258582167 0.1619257999114784 chr6 171115067 4981942 0.02911457235966252 0.2263148916098691 chr7 159138663 5303949 0.033329103688649185 0.5105639796475929 chr8 146364022 10455224 0.07143301924293936 0.32460758412079177 chr9 141213431 2720753 0.019266956271319545 0.17253489666896935 chr10 135534747 4054342 0.029913672248194776 0.20305178682619981 chr11 135006516 3471750 0.025715425468797373 0.18285304023535154 chr12 133851895 2650238 0.019799779450264787 0.15550331503646067 chr13 115169878 1724274 0.014971570951911576 0.13605158170211035 chr14 107349540 1614830 0.015042728641408244 0.13735566233629212 chr15 102531392 1548888 0.015106475878138863 0.14038055078983244 chr16 90354753 2124590 0.02351387093050877 0.17208079787810948 chr17 81195210 1384555 0.01705217586111299 0.14446190089677677 chr18 78077248 2924695 0.03745899189479629 0.2544174228766227 chr19 59128983 1188772 0.020104725968312358 0.17495733092754182 chr20 63025520 2138334 0.0339280659643903 0.20486875519969086 chr21 48129895 1281034 0.026616181065842758 0.1830400146618787 chr22 51304566 764095 0.014893313784196128 0.13424718086159795 chrMT 16571 8609 0.5195220566049122 0.8206669706258518 chrX 155270560 5568421 0.03586269670180876 0.2148046743546225 chrY 59373566 162932 0.002744184171117497 0.06143257713197729