BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080905.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 = 2,923,747 number of mapped reads = 2,626,916 (89.85%) number of supplementary alignments = 23,300 (0.8%) number of secondary alignments = 0 number of mapped bases = 178,910,643 bp number of sequenced bases = 178,844,897 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,487 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7695 >>>>>>> ACTG content number of A's = 51,130,648 bp (28.59%) number of C's = 31,398,319 bp (17.56%) number of T's = 57,735,889 bp (32.28%) number of G's = 37,721,420 bp (21.09%) number of N's = 858,621 bp (0.48%) GC percentage = 38.65% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 2,072,291 number of insertions = 13,903 mapped reads with insertion percentage = 0.53% number of deletions = 39,938 mapped reads with deletion percentage = 1.51% homopolymer indels = 49.71% >>>>>>> Coverage mean coverageData = 0.0578X std coverageData = 0.4633X There is a 4.6% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 14037353 0.05631822678588231 0.7575808172954771 chr2 243199373 15254482 0.06272418309236348 0.45915434606310973 chr3 198022430 13021384 0.06575711650442831 0.3093685422986781 chr4 191154276 12979113 0.06789862759857906 0.3261081121867966 chr5 180915260 11329482 0.06262314190632676 0.3034804906289543 chr6 171115067 10864872 0.06349453727531779 0.39958863280170287 chr7 159138663 9884222 0.06211075180391581 0.6282334591462968 chr8 146364022 9140264 0.06244884415652366 0.8370974041655497 chr9 141213431 7490506 0.05304386379508051 0.4357413110994091 chr10 135534747 8045226 0.05935913983740273 0.39237592541619426 chr11 135006516 8170296 0.06051779011910803 0.42323313195899603 chr12 133851895 8069440 0.06028633363763733 0.29922875205362465 chr13 115169878 6056413 0.052586779678623956 0.2754408911582966 chr14 107349540 5427142 0.050555801170643115 0.29673825017082006 chr15 102531392 4858435 0.047384853606591046 0.26213098337451485 chr16 90354753 4336645 0.04799575955899077 0.28436748542653806 chr17 81195210 3895011 0.04797094557671567 0.3214680410846757 chr18 78077248 4883470 0.06254664611129737 0.7943855522558863 chr19 59128983 2659806 0.044983117670060385 0.5009201446970521 chr20 63025520 3378794 0.05360993451541534 0.295792237996291 chr21 48129895 2320920 0.04822200422419372 0.29160043687118037 chr22 51304566 1560765 0.030421561308987585 0.2069085372255312 chrMT 16571 53947 3.2555066079295156 2.483671534461852 chrX 155270560 10812396 0.06963584081876178 0.3499085894528724 chrY 59373566 380259 0.006404516784455898 0.1371302906692298