BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081890.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,076,341 number of mapped reads = 2,800,234 (91.02%) number of supplementary alignments = 20,918 (0.68%) number of secondary alignments = 0 number of mapped bases = 187,045,121 bp number of sequenced bases = 186,977,860 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,306 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6177 >>>>>>> ACTG content number of A's = 51,383,439 bp (27.48%) number of C's = 36,557,578 bp (19.55%) number of T's = 56,632,742 bp (30.29%) number of G's = 42,401,977 bp (22.68%) number of N's = 2,124 bp (0%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,563,099 number of insertions = 13,773 mapped reads with insertion percentage = 0.49% number of deletions = 37,807 mapped reads with deletion percentage = 1.34% homopolymer indels = 46.03% >>>>>>> Coverage mean coverageData = 0.0604X std coverageData = 0.463X There is a 5.01% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15435410 0.06192726797659613 0.7906787411640125 chr2 243199373 17301974 0.07114316861335 0.5883834007964636 chr3 198022430 13551044 0.06843186400651684 0.3075455005588783 chr4 191154276 12795443 0.06693778066466062 0.34093485316763916 chr5 180915260 11017085 0.0608963832017266 0.2873499455433661 chr6 171115067 10870569 0.06352783066145777 0.32652104522813763 chr7 159138663 10599180 0.06660342496405164 0.6475087389103771 chr8 146364022 9758914 0.06667563426208663 0.5284018713270082 chr9 141213431 7919355 0.05608074914630465 0.4195251719865831 chr10 135534747 8783151 0.0648036846226599 0.551682770094441 chr11 135006516 8832961 0.06542618283698247 0.415866258595018 chr12 133851895 8677775 0.06483117030207156 0.30007141441261853 chr13 115169878 5963794 0.051782585026268764 0.2635896005523991 chr14 107349540 5730843 0.053384886418702863 0.28775963416975037 chr15 102531392 5886382 0.057410534326891804 0.28476959852578587 chr16 90354753 5392065 0.05967660605524537 0.34017960172670736 chr17 81195210 4839765 0.05960653343959576 0.3308961522633003 chr18 78077248 4773063 0.06113257219311828 0.7601059533841035 chr19 59128983 3829929 0.06477244839472379 0.6240622891582197 chr20 63025520 3596048 0.0570570143649747 0.2872547634112524 chr21 48129895 2588064 0.05377248381697072 0.30482237756085556 chr22 51304566 2096718 0.040868058410239744 0.2352025111081729 chrMT 16571 29992 1.8099088769537144 1.5919592439444115 chrX 155270560 6316565 0.04068102156648369 0.277469634902724 chrY 59373566 459032 0.007731251985100575 0.22007441914631864