BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525077.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 = 7,284,967 number of mapped reads = 6,785,613 (93.15%) number of supplementary alignments = 29,207 (0.4%) number of secondary alignments = 0 number of mapped bases = 402,018,855 bp number of sequenced bases = 401,888,465 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 837,290 duplication rate = 8.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1961 >>>>>>> ACTG content number of A's = 105,668,855 bp (26.29%) number of C's = 68,610,575 bp (17.07%) number of T's = 127,967,348 bp (31.84%) number of G's = 99,598,302 bp (24.78%) number of N's = 43,385 bp (0.01%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 1,905,581 number of insertions = 30,199 mapped reads with insertion percentage = 0.44% number of deletions = 79,681 mapped reads with deletion percentage = 1.17% homopolymer indels = 42.54% >>>>>>> Coverage mean coverageData = 0.1299X std coverageData = 1.0033X There is a 8.75% of reference with a coverageData >= 1X There is a 2.55% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 31671829 0.12706820497751137 2.0821786567598384 chr2 243199373 34712643 0.14273327505659317 1.2654003136976322 chr3 198022430 25901223 0.1307994402452288 0.5090251993512616 chr4 191154276 26571510 0.13900557474319852 0.7426399435822834 chr5 180915260 24352713 0.13460839621820736 0.5206307632280979 chr6 171115067 22912176 0.13389923167899645 0.6125924732826535 chr7 159138663 21850899 0.13730729282298923 1.2275478771833952 chr8 146364022 20403434 0.13940197680547478 1.1299795630339544 chr9 141213431 16364856 0.11588739034320326 0.7544041667935483 chr10 135534747 20451188 0.15089258254932958 1.1169260476967613 chr11 135006516 17912896 0.1326817144144361 0.7205624427197633 chr12 133851895 18722234 0.13987276011295918 0.5581296654983847 chr13 115169878 12456646 0.1081588885593853 0.46203555093854515 chr14 107349540 12307056 0.11464470178446969 0.5118753022218282 chr15 102531392 11228708 0.10951483034581252 0.46809766714020246 chr16 90354753 11110572 0.12296610450586921 0.5838749130716686 chr17 81195210 11078842 0.13644698991479917 0.5894336944032342 chr18 78077248 11049660 0.14152214996102322 1.513695651183215 chr19 59128983 8005354 0.13538798730903254 1.429325484114491 chr20 63025520 8988072 0.14261004113889103 0.5757161057989993 chr21 48129895 5344368 0.11104050819142655 0.6469915316406116 chr22 51304566 4808908 0.09373255394071553 0.4285986321911036 chrMT 16571 67057 4.046647758131676 3.319797177574398 chrX 155270560 22348753 0.14393425901213985 0.6655948914793675 chrY 59373566 1397258 0.023533334682979964 0.7514781681120335