BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008680.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 = 1,606,339 number of mapped reads = 1,461,955 (91.01%) number of supplementary alignments = 8,448 (0.53%) number of secondary alignments = 0 number of mapped bases = 96,218,523 bp number of sequenced bases = 96,176,152 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,980 duplication rate = 2.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6255 >>>>>>> ACTG content number of A's = 27,107,910 bp (28.19%) number of C's = 17,430,277 bp (18.12%) number of T's = 30,357,895 bp (31.56%) number of G's = 21,263,112 bp (22.11%) number of N's = 16,958 bp (0.02%) GC percentage = 40.23% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 672,172 number of insertions = 8,197 mapped reads with insertion percentage = 0.56% number of deletions = 25,657 mapped reads with deletion percentage = 1.74% homopolymer indels = 48.52% >>>>>>> Coverage mean coverageData = 0.0311X std coverageData = 0.2963X There is a 2.78% of reference with a coverageData >= 1X There is a 0.23% 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 8279487 0.03321751804181062 0.4565330833015113 chr2 243199373 9269732 0.03811577260933152 0.3511315474004325 chr3 198022430 7768124 0.03922850557888821 0.21784174503460826 chr4 191154276 5481899 0.028677877967009224 0.19016660421280798 chr5 180915260 4304397 0.023792337915552287 0.1671630843685783 chr6 171115067 3689052 0.021558896388709007 0.18018785463698175 chr7 159138663 5268906 0.03310889950105965 0.4302054936077289 chr8 146364022 7486997 0.05115326087445178 0.4098023433662655 chr9 141213431 2876056 0.020366731263685534 0.2777231885614276 chr10 135534747 5117717 0.03775944629165833 0.33599130670481664 chr11 135006516 4623624 0.034247413658167435 0.31503559050399005 chr12 133851895 4365413 0.03261375567376166 0.19798828649099476 chr13 115169878 3097062 0.026891250158309624 0.17683622583997405 chr14 107349540 4056033 0.03778342226710985 0.21595743577588114 chr15 102531392 2309087 0.02252078075756545 0.16290715218408758 chr16 90354753 2338912 0.025885876750722788 0.21208468186923524 chr17 81195210 2685140 0.03307017741563819 0.2499189417155594 chr18 78077248 1545674 0.019796727466623823 0.5333446164128117 chr19 59128983 1294014 0.0218845976092638 0.30449605734863394 chr20 63025520 1455592 0.02309527949947894 0.16835198343431873 chr21 48129895 906588 0.018836276289403913 0.16014160332482175 chr22 51304566 1115074 0.021734400793878658 0.1580072646676821 chrMT 16571 86033 5.191780821917808 3.7267539235669007 chrX 155270560 6529527 0.04205257583923185 0.25099481124369416 chrY 59373566 268383 0.0045202439078697075 0.12245025428266142