BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094085.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 434,754 number of mapped reads = 423,507 (97.41%) number of supplementary alignments = 15,165 (3.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 212,739 number of mapped paired reads (second in pair) = 210,768 number of mapped paired reads (both in pair) = 420,702 number of mapped paired reads (singletons) = 2,805 number of mapped bases = 56,839,592 bp number of sequenced bases = 55,666,621 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 405,674 duplication rate = 49.84% >>>>>>> Insert size mean insert size = 366,507.8082 std insert size = 5,503,842.9979 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 38.76 >>>>>>> ACTG content number of A's = 14,768,038 bp (26.53%) number of C's = 13,113,027 bp (23.56%) number of T's = 14,066,401 bp (25.27%) number of G's = 13,718,425 bp (24.64%) number of N's = 730 bp (0%) GC percentage = 48.2% >>>>>>> Mismatches and indels general error rate = 0.0386 number of mismatches = 2,074,187 number of insertions = 33,195 mapped reads with insertion percentage = 7.71% number of deletions = 169,153 mapped reads with deletion percentage = 38.17% homopolymer indels = 29.88% >>>>>>> Coverage mean coverageData = 0.0184X std coverageData = 4.9984X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 483364 0.0019392689898253051 0.7013860126904053 chr2 243199373 2624232 0.010790455450721907 4.619859328389122 chr3 198022430 963435 0.0048652821804075425 2.213891434300902 chr4 191154276 700190 0.0036629575579046948 1.4908589201406508 chr5 180915260 413541 0.002285827077273636 1.2900320502139777 chr6 171115067 1109265 0.0064825676630801896 3.6066049966675293 chr7 159138663 1664365 0.010458583531017852 4.143652723402297 chr8 146364022 1002296 0.006847967050263213 2.440914588200952 chr9 141213431 722642 0.005117374423117019 2.358836270920083 chr10 135534747 1347527 0.009942299150785296 3.335914301365384 chr11 135006516 1863192 0.01380075610572752 3.72984561934215 chr12 133851895 1734339 0.012957149392617863 3.952495377446948 chr13 115169878 1338201 0.011619366306874095 3.6896952237500584 chr14 107349540 366112 0.003410466407215159 1.441289968679048 chr15 102531392 933903 0.0091084591926734 2.933306341820818 chr16 90354753 304159 0.003366275595927975 1.266340611249867 chr17 81195210 828161 0.010199628771204608 3.54755316806031 chr18 78077248 109001 0.0013960661113465475 0.6358888885881768 chr19 59128983 219099 0.003705441712061917 0.9915186042828084 chr20 63025520 332029 0.005268167561330712 1.8854237794158666 chr21 48129895 868057 0.018035713562225723 7.47818414334037 chr22 51304566 86709 0.0016900834908144433 0.4089736586064779 chrMT 16571 1682553 101.53599662060226 470.4979291704242 chrX 155270560 34594949 0.2228043036619434 17.40810468637082 chrY 59373566 548271 0.009234260916718393 2.8624233607289518