BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818899.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,163,123 number of mapped reads = 1,135,687 (97.64%) number of supplementary alignments = 16,710 (1.44%) number of secondary alignments = 0 number of mapped bases = 105,121,974 bp number of sequenced bases = 105,053,813 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 188,773 duplication rate = 13.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1581 >>>>>>> ACTG content number of A's = 30,648,974 bp (29.17%) number of C's = 22,721,845 bp (21.63%) number of T's = 29,581,023 bp (28.16%) number of G's = 22,100,531 bp (21.04%) number of N's = 1,440 bp (0%) GC percentage = 42.67% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 649,341 number of insertions = 16,121 mapped reads with insertion percentage = 1.37% number of deletions = 35,164 mapped reads with deletion percentage = 3.02% homopolymer indels = 40.83% >>>>>>> Coverage mean coverageData = 0.034X std coverageData = 0.4575X There is a 2.6% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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 9919817 0.03979856483486956 0.6914503032684183 chr2 243199373 7979240 0.032809459586887996 0.6707721987745772 chr3 198022430 6536672 0.033009755511029734 0.2244562889931353 chr4 191154276 5342479 0.027948519446146212 0.272119605658439 chr5 180915260 4663101 0.025775056233509546 0.21168545297606514 chr6 171115067 5195431 0.03036220650283239 0.23783721295133559 chr7 159138663 9458042 0.05943270995056682 0.9818312281940541 chr8 146364022 9099479 0.062170189611214705 0.3765185314588574 chr9 141213431 3883321 0.027499657592768213 0.3489172310390302 chr10 135534747 4936547 0.03642274109974175 0.5911831698742013 chr11 135006516 4624159 0.03425137642986061 0.2730488163266067 chr12 133851895 4034959 0.030144952374413527 0.21653205794542346 chr13 115169878 3179714 0.027608903084884746 0.2021472716126295 chr14 107349540 3091512 0.028798558428848414 0.2266766774803998 chr15 102531392 2908837 0.028370208803953426 0.20791906421489212 chr16 90354753 2643304 0.029254731070981956 0.4933160957242763 chr17 81195210 2602164 0.032048245210524115 0.27258952796257135 chr18 78077248 1981549 0.025379339702137044 0.3993196901610266 chr19 59128983 1864441 0.03153176167430446 0.6000671423270576 chr20 63025520 4292442 0.06810641149807253 0.3432852496782916 chr21 48129895 990691 0.020583693357319813 0.21481640401919672 chr22 51304566 948572 0.01848903662882559 0.18771031303156369 chrMT 16571 244188 14.735863858548067 8.923916779443275 chrX 155270560 4289477 0.027625822950596686 0.24543563061669238 chrY 59373566 411836 0.006936352787029838 0.5799382386133801