BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524658.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 = 1,986,737 number of mapped reads = 1,847,069 (92.97%) number of supplementary alignments = 8,361 (0.42%) number of secondary alignments = 0 number of mapped bases = 109,341,266 bp number of sequenced bases = 109,308,855 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,660 duplication rate = 3.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8572 >>>>>>> ACTG content number of A's = 26,548,141 bp (24.29%) number of C's = 20,619,404 bp (18.86%) number of T's = 34,918,016 bp (31.94%) number of G's = 27,209,190 bp (24.89%) number of N's = 14,104 bp (0.01%) GC percentage = 43.76% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 535,874 number of insertions = 7,221 mapped reads with insertion percentage = 0.39% number of deletions = 20,260 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.72% >>>>>>> Coverage mean coverageData = 0.0353X std coverageData = 0.3271X There is a 3.16% of reference with a coverageData >= 1X There is a 0.27% 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 0.01% 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 8846163 0.03549103695111756 0.6070396186348695 chr2 243199373 9262521 0.038086122039467596 0.4368531302387597 chr3 198022430 7271098 0.03671855758966295 0.20947274381613035 chr4 191154276 7001335 0.03662661985128703 0.23703680526008786 chr5 180915260 6584023 0.03639285597024817 0.20946889511919056 chr6 171115067 6287062 0.03674172070423232 0.24532481720550212 chr7 159138663 6084959 0.038236836261468406 0.40130647257726454 chr8 146364022 5509552 0.037642802682752184 0.3355241035492571 chr9 141213431 4619341 0.03271176804704929 0.26861835249336685 chr10 135534747 5255275 0.038774374220066236 0.32953141983486234 chr11 135006516 4999382 0.03703067191216163 0.2785255118925769 chr12 133851895 4918393 0.0367450382379719 0.21189142973839517 chr13 115169878 3428771 0.029771421655929862 0.19034399117559064 chr14 107349540 3279011 0.030545179793038703 0.20105183068064025 chr15 102531392 3150645 0.030728588957419013 0.19121046563933428 chr16 90354753 3168744 0.035070031124981325 0.22345282501237515 chr17 81195210 2972594 0.036610460149065445 0.2265825194714118 chr18 78077248 2909099 0.037259241001936956 0.5020051441359791 chr19 59128983 2252837 0.03810038471319556 0.45871333165804035 chr20 63025520 2299530 0.03648569658766798 0.21223742839762763 chr21 48129895 1450770 0.030142804176073935 0.21882450888628 chr22 51304566 1310783 0.025549051521067345 0.1757186753779742 chrMT 16571 30794 1.8583066803451813 1.7279201941601916 chrX 155270560 6089763 0.039220332560145336 0.2387330693539888 chrY 59373566 358821 0.00604344701141919 0.22157741633969671