BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240263.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,528,148 number of mapped reads = 2,110,900 (83.5%) number of supplementary alignments = 11,390 (0.45%) number of secondary alignments = 0 number of mapped bases = 132,332,235 bp number of sequenced bases = 132,260,563 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 175,876 duplication rate = 6.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6962 >>>>>>> ACTG content number of A's = 35,801,433 bp (27.07%) number of C's = 23,199,356 bp (17.54%) number of T's = 43,288,787 bp (32.73%) number of G's = 29,938,339 bp (22.64%) number of N's = 32,648 bp (0.02%) GC percentage = 40.18% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,177,197 number of insertions = 9,524 mapped reads with insertion percentage = 0.45% number of deletions = 41,863 mapped reads with deletion percentage = 1.96% homopolymer indels = 48.46% >>>>>>> Coverage mean coverageData = 0.0427X std coverageData = 0.3896X There is a 3.21% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.19% 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 8897065 0.035695257104294234 0.577957867383643 chr2 243199373 12697911 0.05221193970759127 0.4628673982030781 chr3 198022430 9482652 0.047886757070903535 0.2775583591707611 chr4 191154276 8765890 0.045857671528101204 0.27837022177484627 chr5 180915260 7213222 0.039870721795386414 0.2545582211417335 chr6 171115067 7393896 0.043210081552900306 0.34283712989572485 chr7 159138663 8004033 0.05029596736023854 0.6154030959878013 chr8 146364022 8290281 0.05664152219047383 0.6190942405950952 chr9 141213431 4610302 0.032647758554921025 0.33961606443034564 chr10 135534747 6578623 0.04853827631374853 0.3589488094707405 chr11 135006516 6428436 0.04761574619109495 0.3714167739512471 chr12 133851895 5989141 0.0447445364893788 0.2750420751983909 chr13 115169878 2937230 0.025503456728503265 0.1997228575579232 chr14 107349540 5117414 0.04767057222601979 0.2937222095391808 chr15 102531392 3183850 0.031052440992900984 0.23401007732740264 chr16 90354753 4111591 0.04550497747473229 0.28571796786388115 chr17 81195210 3441187 0.04238165034612264 0.29174325950294905 chr18 78077248 2880934 0.03689850851300497 0.5509495002389985 chr19 59128983 2462039 0.041638446580418945 0.4176999472154363 chr20 63025520 2835302 0.044986570519370564 0.27361399558852745 chr21 48129895 2678795 0.055657611553069045 0.3159944941254278 chr22 51304566 1152565 0.02246515446597872 0.18420892392158994 chrMT 16571 31861 1.922696276627844 2.136272708711867 chrX 155270560 6860238 0.044182477347927386 0.29782835413818676 chrY 59373566 287777 0.004846887586303979 0.10139980725705354