BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525134.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,951,374 number of mapped reads = 1,782,937 (91.37%) number of supplementary alignments = 50,550 (2.59%) number of secondary alignments = 0 number of mapped bases = 137,707,902 bp number of sequenced bases = 137,653,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,500 duplication rate = 2.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8205 >>>>>>> ACTG content number of A's = 35,866,258 bp (26.06%) number of C's = 27,015,347 bp (19.63%) number of T's = 42,398,808 bp (30.8%) number of G's = 32,368,523 bp (23.51%) number of N's = 4,887 bp (0%) GC percentage = 43.14% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,024,398 number of insertions = 11,542 mapped reads with insertion percentage = 0.64% number of deletions = 31,631 mapped reads with deletion percentage = 1.75% homopolymer indels = 43.12% >>>>>>> Coverage mean coverageData = 0.0445X std coverageData = 0.4775X There is a 3.84% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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% 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 13303056 0.053372208047577946 0.8480929567940885 chr2 243199373 11474540 0.047181618350636126 0.6845449583663761 chr3 198022430 9003365 0.0454663898428072 0.2415380848278893 chr4 191154276 8702567 0.04552640506979818 0.2549628572718838 chr5 180915260 8131673 0.04494741350176873 0.24132621046125427 chr6 171115067 7736854 0.04521433521689823 0.28187305586601547 chr7 159138663 7334775 0.04609046514359619 0.6787610909066378 chr8 146364022 6848688 0.04679215497371342 0.5880854419364342 chr9 141213431 5568133 0.03943061903226471 0.4251964249867632 chr10 135534747 6309685 0.04655400286392979 0.48702348293403647 chr11 135006516 7460738 0.05526205861056366 0.546478453061414 chr12 133851895 5998674 0.04481575699768763 0.2398024718885247 chr13 115169878 4996815 0.04338647471693944 0.23373703464871987 chr14 107349540 4014408 0.03739567025624889 0.25761928375345305 chr15 102531392 3700118 0.03608765986518549 0.21079729726171859 chr16 90354753 2992899 0.03312386897897889 0.2408213723872672 chr17 81195210 3978713 0.04900181919598459 0.30228747262500355 chr18 78077248 3708024 0.04749173536444317 0.8205018043394937 chr19 59128983 2580946 0.04364942316021231 0.5944924480447599 chr20 63025520 2600457 0.04126038150895066 0.24341188553008397 chr21 48129895 1774769 0.036874566212953507 0.2428307865653297 chr22 51304566 1388735 0.027068448449598034 0.18115460769211045 chrMT 16571 12875 0.7769597489590248 1.4323108202936938 chrX 155270560 7741267 0.049856630902857565 0.36944136384164433 chrY 59373566 345128 0.005812822494104531 0.12920919316716356