BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083658.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 = 2,231,378 number of mapped reads = 1,853,587 (83.07%) number of supplementary alignments = 13,916 (0.62%) number of secondary alignments = 0 number of mapped bases = 112,868,027 bp number of sequenced bases = 112,831,451 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,653 duplication rate = 2.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3444 >>>>>>> ACTG content number of A's = 33,232,253 bp (29.45%) number of C's = 21,999,532 bp (19.5%) number of T's = 33,241,868 bp (29.46%) number of G's = 24,341,868 bp (21.57%) number of N's = 15,930 bp (0.01%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 921,505 number of insertions = 8,046 mapped reads with insertion percentage = 0.43% number of deletions = 23,223 mapped reads with deletion percentage = 1.24% homopolymer indels = 45.56% >>>>>>> Coverage mean coverageData = 0.0365X std coverageData = 0.3866X There is a 3.27% of reference with a coverageData >= 1X There is a 0.29% 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 12136061 0.0486901936344624 0.995953346516045 chr2 243199373 9996839 0.04110552949493007 0.27190051096398105 chr3 198022430 8982794 0.04536250767147944 0.23177887887456383 chr4 191154276 5298912 0.02772060406328551 0.18177185785777134 chr5 180915260 5864189 0.032414009741356255 0.19611745364170857 chr6 171115067 8111681 0.04740483197777084 0.2833634612489427 chr7 159138663 7990610 0.050211619535850946 0.5274410122370722 chr8 146364022 7843560 0.05358939917625385 0.40728775604227624 chr9 141213431 4191798 0.029684131107897235 0.21470456998197737 chr10 135534747 5098689 0.03761905424887096 0.27455731510206466 chr11 135006516 4301479 0.03186126957012949 0.21857739742368465 chr12 133851895 3752075 0.02803154187693794 0.1824209777795797 chr13 115169878 2956923 0.02567444761902066 0.17192167881381593 chr14 107349540 2015786 0.01877777957874808 0.15031222536429545 chr15 102531392 2874550 0.028035803902867133 0.18142624856839773 chr16 90354753 3047789 0.03373136330747316 0.20418907547760154 chr17 81195210 2340943 0.028831048038424928 0.1899709920625458 chr18 78077248 2521117 0.03229003409546402 0.34911073738455534 chr19 59128983 3087739 0.0522203975671288 0.6483616103787302 chr20 63025520 2334265 0.03703682254426461 0.2123926826789436 chr21 48129895 1766141 0.03669530132986993 0.21005683804994119 chr22 51304566 924948 0.01802857079036591 0.14338533944135243 chrMT 16571 8250 0.4978577032164625 0.708605381373846 chrX 155270560 5217338 0.03360159195664651 0.20792193574680173 chrY 59373566 203551 0.0034283101675247197 0.07215857582168596