BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716340.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 = 1,717,597 number of mapped reads = 1,575,653 (91.74%) number of supplementary alignments = 10,084 (0.59%) number of secondary alignments = 0 number of mapped bases = 91,682,350 bp number of sequenced bases = 91,655,776 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,860 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7782 >>>>>>> ACTG content number of A's = 22,899,613 bp (24.98%) number of C's = 17,834,019 bp (19.46%) number of T's = 28,634,351 bp (31.24%) number of G's = 22,286,665 bp (24.32%) number of N's = 1,128 bp (0%) GC percentage = 43.77% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 452,820 number of insertions = 6,836 mapped reads with insertion percentage = 0.43% number of deletions = 16,462 mapped reads with deletion percentage = 1.04% homopolymer indels = 41.79% >>>>>>> Coverage mean coverageData = 0.0296X std coverageData = 0.2579X There is a 2.64% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7339966 0.029448135256601827 0.4100051884487751 chr2 243199373 7764646 0.031927080667268 0.3462835929627573 chr3 198022430 6056775 0.030586307823815717 0.19230201394172727 chr4 191154276 5832997 0.030514603816657493 0.21300762952822383 chr5 180915260 5474411 0.03025953145135463 0.19211361134480323 chr6 171115067 5216303 0.03048418290365979 0.21047390720050374 chr7 159138663 5061452 0.03180529422947333 0.3321515831688224 chr8 146364022 4603188 0.0314502699304068 0.25931853655761145 chr9 141213431 3799977 0.02690945877520673 0.21599017084391978 chr10 135534747 4408058 0.03252345319241272 0.26592549620088807 chr11 135006516 4152157 0.030755234065887604 0.2364310049963573 chr12 133851895 4144385 0.03096246788287906 0.19703780187000255 chr13 115169878 2849119 0.024738404255320996 0.1734285554838538 chr14 107349540 2796757 0.026052808423771542 0.18614931842027405 chr15 102531392 2694203 0.026276859676302843 0.18203569540386383 chr16 90354753 2675431 0.029610296206553737 0.19576910177865214 chr17 81195210 2599512 0.032015583185264256 0.21259071824645956 chr18 78077248 2419679 0.03099083359085607 0.36239626662615765 chr19 59128983 1969647 0.03331102447677817 0.325368237034429 chr20 63025520 2001328 0.03175424812044391 0.1995445429989348 chr21 48129895 1195763 0.024844496336424587 0.18896073404229125 chr22 51304566 1165588 0.022718991522119102 0.16563976347262466 chrMT 16571 8366 0.5048578842556273 0.8146851080276633 chrX 155270560 5167168 0.033278478547382064 0.2165482808973423 chrY 59373566 285474 0.0048080992810841106 0.1296541097205235