BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716165.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 = 2,227,310 number of mapped reads = 2,022,464 (90.8%) number of supplementary alignments = 9,874 (0.44%) number of secondary alignments = 0 number of mapped bases = 116,469,417 bp number of sequenced bases = 116,436,770 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,961 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3253 >>>>>>> ACTG content number of A's = 30,431,574 bp (26.14%) number of C's = 22,536,321 bp (19.35%) number of T's = 36,334,155 bp (31.21%) number of G's = 27,132,842 bp (23.3%) number of N's = 1,878 bp (0%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 622,181 number of insertions = 8,934 mapped reads with insertion percentage = 0.44% number of deletions = 19,769 mapped reads with deletion percentage = 0.97% homopolymer indels = 41.84% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 0.3602X There is a 3.32% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% 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% 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 8308272 0.03333300421345791 0.6624603493761736 chr2 243199373 9107612 0.03744915904861317 0.39827050825988114 chr3 198022430 7080816 0.0357576462423979 0.20573692663951484 chr4 191154276 7273155 0.03804861262951816 0.24054212355818716 chr5 180915260 6478423 0.03580915728170194 0.2119452074774809 chr6 171115067 6146045 0.03591761443193077 0.23967917572344952 chr7 159138663 7540144 0.04738096863362488 0.4885720045088703 chr8 146364022 5109124 0.03490696641282514 0.33289541577063075 chr9 141213431 5313359 0.03762644220435378 0.3792228978491161 chr10 135534747 4461515 0.03291786865548212 0.3587829274277455 chr11 135006516 4489519 0.03325409123215949 0.2865805330473067 chr12 133851895 8769588 0.06551710007542291 0.3194647687463451 chr13 115169878 4383585 0.03806190538814325 0.21251638924011185 chr14 107349540 4135146 0.038520388629518114 0.24811646900073805 chr15 102531392 2949025 0.028762166810336488 0.18634960963579802 chr16 90354753 3261597 0.036097680439677586 0.23787491122735283 chr17 81195210 3514353 0.043282762616169104 0.23804220773866758 chr18 78077248 3705617 0.04746090692130952 0.7059221180328102 chr19 59128983 1998600 0.033800682822500094 0.4993389752962973 chr20 63025520 3516755 0.055798904951518055 0.26871223696265056 chr21 48129895 1391666 0.028914794017315018 0.2220412246375231 chr22 51304566 1124490 0.021917932216793334 0.15964218566195876 chrMT 16571 4941 0.29817150443545953 0.5917040887109127 chrX 155270560 6091865 0.039233870219827896 0.2709202127064585 chrY 59373566 314205 0.005292001494402408 0.12363715864791928