BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525117.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 = 2,032,154 number of mapped reads = 1,829,710 (90.04%) number of supplementary alignments = 47,790 (2.35%) number of secondary alignments = 0 number of mapped bases = 138,109,032 bp number of sequenced bases = 138,057,549 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,111 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2491 >>>>>>> ACTG content number of A's = 37,176,259 bp (26.93%) number of C's = 27,257,233 bp (19.74%) number of T's = 42,207,251 bp (30.57%) number of G's = 31,411,898 bp (22.75%) number of N's = 4,908 bp (0%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,003,372 number of insertions = 10,710 mapped reads with insertion percentage = 0.58% number of deletions = 30,112 mapped reads with deletion percentage = 1.62% homopolymer indels = 42.85% >>>>>>> Coverage mean coverageData = 0.0446X std coverageData = 0.4393X There is a 3.87% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10919316 0.04380858092225175 0.6562604385961454 chr2 243199373 11965554 0.04920059559528552 0.6591428855706721 chr3 198022430 9365996 0.0472976520892103 0.24252710426784657 chr4 191154276 9084065 0.04752216476705967 0.255893781062977 chr5 180915260 8452845 0.04672267557750518 0.24827421950851522 chr6 171115067 8114324 0.04742027772457933 0.2866945203089928 chr7 159138663 7836901 0.0492457386047035 0.6915161940703178 chr8 146364022 7296839 0.04985404814852656 0.6266001159907627 chr9 141213431 5812683 0.041162394814980456 0.4313006561587979 chr10 135534747 6324127 0.0466605585651036 0.41239411063075726 chr11 135006516 6092175 0.04512504418675614 0.44714461526067784 chr12 133851895 6286291 0.046964527472696596 0.24484758559645925 chr13 115169878 4455452 0.038685914037349244 0.2180092166557805 chr14 107349540 4161213 0.038763212213112415 0.27541436796471547 chr15 102531392 3821431 0.03727083896412915 0.2156508856680768 chr16 90354753 3844787 0.04255212783327513 0.2579010068068983 chr17 81195210 3410982 0.042009645642889525 0.28754884890934634 chr18 78077248 3871959 0.049591386725105886 0.731754122181793 chr19 59128983 2622628 0.044354356644354935 0.4962609786521895 chr20 63025520 2780997 0.044124935422984214 0.24078556831275222 chr21 48129895 1774445 0.03686783443013952 0.2364553319545247 chr22 51304566 1414084 0.027562537026431525 0.18382730906606312 chrMT 16571 9114 0.5499969826805866 0.9570313300701577 chrX 155270560 8070909 0.05197964765503518 0.363924479295752 chrY 59373566 319915 0.005388172238130349 0.11654236885241466