BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524409.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 = 2,009,328 number of mapped reads = 1,850,865 (92.11%) number of supplementary alignments = 7,413 (0.37%) number of secondary alignments = 0 number of mapped bases = 107,988,549 bp number of sequenced bases = 107,957,681 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,886 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7538 >>>>>>> ACTG content number of A's = 26,962,113 bp (24.97%) number of C's = 19,038,761 bp (17.64%) number of T's = 35,640,947 bp (33.01%) number of G's = 26,301,922 bp (24.36%) number of N's = 13,938 bp (0.01%) GC percentage = 42% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 526,933 number of insertions = 7,243 mapped reads with insertion percentage = 0.39% number of deletions = 19,586 mapped reads with deletion percentage = 1.05% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.0349X std coverageData = 0.342X There is a 3.07% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% 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 8987841 0.03605945278667932 0.7295710223405169 chr2 243199373 8896964 0.03658300549977158 0.3841910843910248 chr3 198022430 7572928 0.03824277886096035 0.21619154009648867 chr4 191154276 7000950 0.036624605771309035 0.24010146460088064 chr5 180915260 6891690 0.03809346983775719 0.21737315556365125 chr6 171115067 3952415 0.02309799522212734 0.18919707187735188 chr7 159138663 6256835 0.03931687549743961 0.47866581380629986 chr8 146364022 5618468 0.03838694730594381 0.31180082810741955 chr9 141213431 4068288 0.028809497589503366 0.25236770362973915 chr10 135534747 5310241 0.039179923359431955 0.300568749229428 chr11 135006516 4489309 0.03325253575168179 0.2653918455264826 chr12 133851895 4988200 0.03726656241960564 0.22244160378516314 chr13 115169878 3532435 0.030671518120389082 0.19364982697319966 chr14 107349540 3086396 0.02875090102854656 0.19321884941496198 chr15 102531392 3321032 0.03239039220300452 0.19937615729791264 chr16 90354753 3134240 0.03468815857423682 0.21671113220656152 chr17 81195210 2946131 0.036284541908321935 0.2334731754594427 chr18 78077248 3070862 0.039331073759157086 0.4497276717799872 chr19 59128983 2948264 0.04986157127038698 0.5068214748956072 chr20 63025520 2986030 0.04737810969270861 0.24945621982299784 chr21 48129895 1491286 0.030984609461541524 0.2148249876037497 chr22 51304566 743131 0.014484695182880994 0.13275288166017432 chrMT 16571 3689 0.22261782632309457 0.5085570845944809 chrX 155270560 6368719 0.041016912671661646 0.25254983452696683 chrY 59373566 322205 0.0054267415906937445 0.14663913926118924