BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818813.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 = 800,019 number of mapped reads = 778,266 (97.28%) number of supplementary alignments = 6,478 (0.81%) number of secondary alignments = 0 number of mapped bases = 52,865,163 bp number of sequenced bases = 52,843,392 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 217,055 duplication rate = 25.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7464 >>>>>>> ACTG content number of A's = 15,306,229 bp (28.97%) number of C's = 11,734,803 bp (22.21%) number of T's = 14,812,511 bp (28.03%) number of G's = 10,986,471 bp (20.79%) number of N's = 3,378 bp (0.01%) GC percentage = 43% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 271,603 number of insertions = 6,348 mapped reads with insertion percentage = 0.81% number of deletions = 13,489 mapped reads with deletion percentage = 1.71% homopolymer indels = 42.04% >>>>>>> Coverage mean coverageData = 0.0171X std coverageData = 0.2285X There is a 1.13% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.13% 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 4539897 0.018214185311899382 0.3081835466287547 chr2 243199373 4674859 0.019222331629942156 0.33384528557248005 chr3 198022430 3626134 0.01831173367582652 0.1908978473395936 chr4 191154276 3355723 0.017555050664940397 0.20335657743340788 chr5 180915260 3092612 0.017094257278241758 0.18948316647104885 chr6 171115067 3087206 0.018041695884091845 0.19518618162816373 chr7 159138663 2953768 0.018560970315554304 0.2159624820923923 chr8 146364022 2644325 0.018066769168177135 0.20374101104541406 chr9 141213431 2278625 0.016136035955390107 0.20795549324346765 chr10 135534747 2427145 0.01790791700079685 0.23227663499477003 chr11 135006516 2589365 0.019179555748257367 0.21002379724442197 chr12 133851895 2570846 0.01920664627123882 0.20121966067599648 chr13 115169878 1645653 0.014288918496553412 0.16941289579326632 chr14 107349540 1645349 0.015327024223857877 0.1827524634483165 chr15 102531392 1648013 0.01607325296042016 0.17986350407969853 chr16 90354753 1630694 0.018047683667509997 0.2710091805108813 chr17 81195210 1580937 0.019470816074002396 0.20723520255236613 chr18 78077248 1284009 0.01644536702932972 0.228996118672734 chr19 59128983 1168435 0.019760782964929398 0.26481611118494314 chr20 63025520 1125567 0.017858908581793533 0.19892192829808467 chr21 48129895 718942 0.0149375351847329 0.17766865161670958 chr22 51304566 721956 0.014071963887190859 0.17988765322715675 chrMT 16571 68130 4.1113994327439505 4.030882289916481 chrX 155270560 1311046 0.00844362253861904 0.14068325908347454 chrY 59373566 475927 0.008015806225955841 0.33134642855887414