BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082773.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 = 4,780,500 number of mapped reads = 4,263,547 (89.19%) number of supplementary alignments = 32,192 (0.67%) number of secondary alignments = 0 number of mapped bases = 293,876,430 bp number of sequenced bases = 293,764,949 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 233,555 duplication rate = 4.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5262 >>>>>>> ACTG content number of A's = 84,107,662 bp (28.63%) number of C's = 54,021,732 bp (18.39%) number of T's = 94,897,174 bp (32.3%) number of G's = 60,721,724 bp (20.67%) number of N's = 16,657 bp (0.01%) GC percentage = 39.06% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 2,503,486 number of insertions = 22,826 mapped reads with insertion percentage = 0.53% number of deletions = 64,634 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.11% >>>>>>> Coverage mean coverageData = 0.0949X std coverageData = 0.6306X There is a 6.83% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.16% 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 0.01% 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 29399261 0.11795060281916007 1.1551130841068054 chr2 243199373 31334542 0.12884302131815117 0.7593445853822464 chr3 198022430 21687555 0.10952069924603995 0.43336396508925334 chr4 191154276 17928789 0.09379224663538262 0.42009958100355116 chr5 180915260 14462695 0.0799418191699252 0.36945518281543904 chr6 171115067 21261444 0.12425231963939212 0.68349879638127 chr7 159138663 15527315 0.09757097808469084 0.6044641572217895 chr8 146364022 23371085 0.15967779978060456 0.9230812133423935 chr9 141213431 8676190 0.061440260593909085 0.5617846733392281 chr10 135534747 10597160 0.07818777276354084 0.49769531012718177 chr11 135006516 12170713 0.09014907843411055 0.5034642954294105 chr12 133851895 9602756 0.0717416514723232 0.3577548963910867 chr13 115169878 7340771 0.06373863659037653 0.32757681410125383 chr14 107349540 6302981 0.05871455993197549 0.348886798640567 chr15 102531392 5777121 0.05634489971617668 0.3036728952789939 chr16 90354753 8344748 0.09235538500116314 0.43851509986267884 chr17 81195210 7236089 0.08911965373326826 0.4400159744637068 chr18 78077248 10322737 0.13221184486420423 1.1891599900195642 chr19 59128983 4682826 0.07919679592662705 0.7604058635598773 chr20 63025520 5845428 0.0927470015320778 0.41581612091478193 chr21 48129895 5251614 0.10911334836695571 0.44188722529026764 chr22 51304566 3874283 0.07551536446093317 0.35408575626310884 chrMT 16571 14586 0.8802124192867057 1.2130668319819404 chrX 155270560 12383372 0.07975350897169431 0.41532058675939626 chrY 59373566 480369 0.008090620664421604 0.157865988558672