BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083640.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 = 2,245,435 number of mapped reads = 1,811,480 (80.67%) number of supplementary alignments = 12,918 (0.58%) number of secondary alignments = 0 number of mapped bases = 107,961,050 bp number of sequenced bases = 107,925,314 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,205 duplication rate = 2.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2184 >>>>>>> ACTG content number of A's = 32,007,173 bp (29.66%) number of C's = 21,056,290 bp (19.51%) number of T's = 31,519,142 bp (29.2%) number of G's = 23,327,748 bp (21.61%) number of N's = 14,961 bp (0.01%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 913,044 number of insertions = 7,994 mapped reads with insertion percentage = 0.44% number of deletions = 22,392 mapped reads with deletion percentage = 1.22% homopolymer indels = 45.29% >>>>>>> Coverage mean coverageData = 0.0349X std coverageData = 0.2881X There is a 3.13% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.03% 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 9322900 0.037403718243895566 0.524533481227451 chr2 243199373 9573918 0.03936654063659942 0.2822788391752854 chr3 198022430 7025600 0.03547880914298446 0.20460230033891205 chr4 191154276 7340675 0.038401835175269634 0.22134324632310517 chr5 180915260 6180926 0.034164757577663706 0.20095681901084975 chr6 171115067 6740806 0.039393410049624676 0.23880861352519642 chr7 159138663 6213045 0.039041706665588864 0.37429068472898896 chr8 146364022 5794895 0.039592345993334346 0.37956751379747017 chr9 141213431 4525369 0.03204630726662253 0.24897637578881787 chr10 135534747 5367179 0.03960002227325514 0.294347888211979 chr11 135006516 4996904 0.037012317242524795 0.23319792455361568 chr12 133851895 5060765 0.03780869146454744 0.21388828461039408 chr13 115169878 3234690 0.028086250121754926 0.1811276048912888 chr14 107349540 3461367 0.03224389224210928 0.20432832231093437 chr15 102531392 3488302 0.03402179500303673 0.20069029177686934 chr16 90354753 3016321 0.03338309164543895 0.21514035851280874 chr17 81195210 2767003 0.03407840191558098 0.2145837482153063 chr18 78077248 3062762 0.039227330348528676 0.4345300216386868 chr19 59128983 1960085 0.0331493102122186 0.3980714151618028 chr20 63025520 2178459 0.03456471283378543 0.20726649433329183 chr21 48129895 1537132 0.03193715672972069 0.20456633518326126 chr22 51304566 1191875 0.023231363072050936 0.16437527180927797 chrMT 16571 25001 1.5087200531048217 1.510240568156116 chrX 155270560 3625617 0.023350318308892556 0.1818471614893903 chrY 59373566 269454 0.00453828223826071 0.1353893127223794