BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008829.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 = 1,546,895 number of mapped reads = 1,165,942 (75.37%) number of supplementary alignments = 12,305 (0.8%) number of secondary alignments = 0 number of mapped bases = 75,966,204 bp number of sequenced bases = 75,931,032 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 136,263 duplication rate = 9.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3544 >>>>>>> ACTG content number of A's = 21,163,338 bp (27.87%) number of C's = 14,174,839 bp (18.67%) number of T's = 23,914,604 bp (31.5%) number of G's = 16,578,653 bp (21.83%) number of N's = 99,598 bp (0.13%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 630,994 number of insertions = 5,082 mapped reads with insertion percentage = 0.43% number of deletions = 20,264 mapped reads with deletion percentage = 1.72% homopolymer indels = 46.53% >>>>>>> Coverage mean coverageData = 0.0245X std coverageData = 0.3042X There is a 1.36% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 5789034 0.02322575557394499 0.3272903550809202 chr2 243199373 18288952 0.07520147677354415 0.5319003576010584 chr3 198022430 4000003 0.020199747069056775 0.2305187528199911 chr4 191154276 3356146 0.017557263537227908 0.23414767838391826 chr5 180915260 4566690 0.0252421492802763 0.2694769791448356 chr6 171115067 2161144 0.012629770352133866 0.19429950956451303 chr7 159138663 2384264 0.014982305085722632 0.22651947955868199 chr8 146364022 3611044 0.024671664188074854 0.3038390556055173 chr9 141213431 2408794 0.017057825044984567 0.27446734664426437 chr10 135534747 2950505 0.021769362213809276 0.29133252222546563 chr11 135006516 3572706 0.026463211597875763 0.30858473356028004 chr12 133851895 4487379 0.03352495681887806 0.2976145741028844 chr13 115169878 784889 0.006815054540563115 0.13783320919343742 chr14 107349540 6315333 0.05882962330346269 0.4219939516674389 chr15 102531392 1229916 0.011995506702961763 0.22316588551076938 chr16 90354753 1186475 0.013131295926402454 0.19754846468610582 chr17 81195210 962873 0.01185874142083012 0.17521329615099354 chr18 78077248 1484892 0.019018242036399645 0.5041745777829582 chr19 59128983 670939 0.011347041094889118 0.24123691604231087 chr20 63025520 1038359 0.016475215119208853 0.20610280083916774 chr21 48129895 500392 0.010396698351409243 0.15903911565294618 chr22 51304566 437617 0.00852978660807695 0.14199458302245846 chrMT 16571 316126 19.077062337819083 13.998123599033498 chrX 155270560 3276507 0.021101920415563646 0.25344171973562607 chrY 59373566 185225 0.0031196542919453415 0.1318439555601862