BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716568.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 = 2,530,286 number of mapped reads = 2,395,770 (94.68%) number of supplementary alignments = 57,376 (2.27%) number of secondary alignments = 0 number of mapped bases = 187,356,909 bp number of sequenced bases = 187,282,524 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 179,675 duplication rate = 5.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2529 >>>>>>> ACTG content number of A's = 46,496,706 bp (24.83%) number of C's = 38,259,783 bp (20.43%) number of T's = 56,196,050 bp (30.01%) number of G's = 46,321,879 bp (24.73%) number of N's = 8,106 bp (0%) GC percentage = 45.16% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,234,601 number of insertions = 17,258 mapped reads with insertion percentage = 0.71% number of deletions = 35,512 mapped reads with deletion percentage = 1.45% homopolymer indels = 39.14% >>>>>>> Coverage mean coverageData = 0.0605X std coverageData = 0.4431X There is a 4.7% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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% 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 15754180 0.06320618154046645 0.64640436497958 chr2 243199373 15599729 0.06414378790359793 0.5088165102839439 chr3 198022430 11443513 0.05778897370363549 0.2945419119442642 chr4 191154276 10959361 0.05733254431619411 0.4714024738914014 chr5 180915260 11160492 0.06168905818116172 0.30774095700264775 chr6 171115067 10107196 0.05906666301921852 0.3120931628714199 chr7 159138663 10208474 0.0641482956281969 0.5675274942800518 chr8 146364022 9493868 0.06486476574140604 0.4650016513573673 chr9 141213431 7581818 0.0536904878403528 0.3888796101808053 chr10 135534747 9324356 0.06879679348942157 0.6028912279481313 chr11 135006516 8337042 0.06175288606069947 0.45470441573680076 chr12 133851895 8408849 0.06282203923971341 0.31402803989046246 chr13 115169878 6571067 0.05705543076115788 0.29664392976668497 chr14 107349540 5531804 0.0515307657582883 0.31590899941706346 chr15 102531392 5154677 0.050274134579193074 0.27803945047212275 chr16 90354753 6969589 0.07713583147086905 0.3783079640561914 chr17 81195210 5369398 0.066129492121518 0.36374546748223513 chr18 78077248 4776663 0.0611786803756198 0.6349985454013072 chr19 59128983 4759822 0.08049896613307217 0.5425076742815896 chr20 63025520 4211150 0.0668165847739138 0.3517164534762144 chr21 48129895 2568874 0.05337377112499414 0.40546589877438743 chr22 51304566 2369975 0.04619423152317476 0.2701637722174433 chrMT 16571 3980 0.24017862530927525 0.514123093963039 chrX 155270560 10016504 0.06451000112320068 0.3465723180859672 chrY 59373566 674528 0.011360745958900296 0.46642160940352784