BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714052.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 478,152 number of mapped reads = 73,861 (15.45%) number of supplementary alignments = 1,329 (0.28%) number of secondary alignments = 0 number of mapped bases = 7,560,238 bp number of sequenced bases = 7,534,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,020 duplication rate = 35.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 10.8671 >>>>>>> ACTG content number of A's = 264,713 bp (3.51%) number of C's = 142,436 bp (1.89%) number of T's = 171,395 bp (2.27%) number of G's = 6,955,403 bp (92.32%) number of N's = 161 bp (0%) GC percentage = 94.21% >>>>>>> Mismatches and indels general error rate = 0.033 number of mismatches = 194,884 number of insertions = 7,925 mapped reads with insertion percentage = 7.69% number of deletions = 4,810 mapped reads with deletion percentage = 6.32% homopolymer indels = 57.64% >>>>>>> Coverage mean coverageData = 0.0024X std coverageData = 8.8266X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 50418 2.0227833253823668E-4 0.41426446875670125 chr2 243199373 6907939 0.028404427670954562 31.483845954113114 chr3 198022430 8806 4.446970982024612E-5 0.014892821733355833 chr4 191154276 19527 1.0215309020866475E-4 0.048043227357412656 chr5 180915260 9237 5.105705289868859E-5 0.01954890972252378 chr6 171115067 7102 4.1504235275786674E-5 0.01648044259394871 chr7 159138663 14383 9.038029934937935E-5 0.08892690639071064 chr8 146364022 15423 1.0537425652323219E-4 0.041759143574190694 chr9 141213431 7839 5.55117168706141E-5 0.023345429368137938 chr10 135534747 41545 3.0652656178271393E-4 0.5506262610293682 chr11 135006516 8832 6.541906466203453E-5 0.03691005699404098 chr12 133851895 14612 1.0916543243560355E-4 0.059384322567820155 chr13 115169878 2094 1.8181837441904733E-5 0.0052031452591547065 chr14 107349540 15888 1.480024972626804E-4 0.0960230570923851 chr15 102531392 5924 5.777742683918697E-5 0.02012980763740908 chr16 90354753 8621 9.541280025412719E-5 0.037592823409452324 chr17 81195210 15059 1.8546660572711125E-4 0.12007921622132496 chr18 78077248 1692 2.1670845775711766E-5 0.006775159601101326 chr19 59128983 3279 5.545503801409877E-5 0.016096320177372447 chr20 63025520 7479 1.1866621647865817E-4 0.03708442021042071 chr21 48129895 868 1.803452926710104E-5 0.006115428698529085 chr22 51304566 995 1.9393985322865805E-5 0.006040497462304348 chrMT 16571 2133 0.1287188461770563 1.5594682913373015 chrX 155270560 388335 0.00250102144282857 0.4033017068122056 chrY 59373566 2208 3.7188266576408765E-5 0.015057640556236823