BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085121.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 = 2,424,947 number of mapped reads = 2,198,520 (90.66%) number of supplementary alignments = 20,923 (0.86%) number of secondary alignments = 0 number of mapped bases = 149,255,188 bp number of sequenced bases = 149,201,642 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,767 duplication rate = 2.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1379 >>>>>>> ACTG content number of A's = 42,440,334 bp (28.44%) number of C's = 27,818,580 bp (18.64%) number of T's = 46,626,986 bp (31.25%) number of G's = 32,288,221 bp (21.64%) number of N's = 27,521 bp (0.02%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,329,313 number of insertions = 11,973 mapped reads with insertion percentage = 0.54% number of deletions = 32,699 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.3% >>>>>>> Coverage mean coverageData = 0.0482X std coverageData = 0.4211X There is a 4.24% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 11449108 0.04593412026042655 0.7133426106713292 chr2 243199373 12672935 0.05210924207440288 0.4583860843500017 chr3 198022430 10244988 0.051736502779003365 0.2507179668322904 chr4 191154276 10052335 0.052587549754837815 0.2615077290235669 chr5 180915260 9413786 0.05203422862173152 0.2519419476267531 chr6 171115067 8741753 0.05108698581171698 0.297805905694411 chr7 159138663 8224252 0.05167978569733239 0.5333812191689168 chr8 146364022 7739316 0.05287717496585329 0.8243704627825409 chr9 141213431 6410003 0.04539230407906455 0.37984193233972635 chr10 135534747 7043596 0.05196893162754788 0.37927905100766857 chr11 135006516 6626559 0.04908325313720413 0.33866195494231066 chr12 133851895 6821845 0.050965621368304126 0.2534931111865999 chr13 115169878 5043180 0.043789053939954685 0.23231294686293932 chr14 107349540 4604402 0.042891678902396785 0.24904568772621108 chr15 102531392 4187650 0.04084261335299144 0.22678182863723823 chr16 90354753 3968977 0.0439265989692872 0.261928942972043 chr17 81195210 3793169 0.04671665976355009 0.26119755628483715 chr18 78077248 4103030 0.05255090445810795 0.717973910874057 chr19 59128983 2699613 0.04565634081682075 0.5401706593772604 chr20 63025520 2842629 0.04510282501437513 0.23907336129288592 chr21 48129895 1957171 0.040664352166153696 0.23603627229055582 chr22 51304566 1522315 0.02967211534349594 0.18825593392537307 chrMT 16571 9205 0.5554885040130348 0.7969163647008671 chrX 155270560 8720903 0.0561658501135051 0.29352436103561613 chrY 59373566 362468 0.006104871652816002 0.1291042285298768