BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525143.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 = 1,418,900 number of mapped reads = 1,275,161 (89.87%) number of supplementary alignments = 35,001 (2.47%) number of secondary alignments = 0 number of mapped bases = 97,118,303 bp number of sequenced bases = 97,077,608 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,136 duplication rate = 1.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9794 >>>>>>> ACTG content number of A's = 25,483,263 bp (26.25%) number of C's = 19,421,007 bp (20.01%) number of T's = 29,417,636 bp (30.3%) number of G's = 22,752,020 bp (23.44%) number of N's = 3,682 bp (0%) GC percentage = 43.44% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 708,815 number of insertions = 8,190 mapped reads with insertion percentage = 0.63% number of deletions = 23,827 mapped reads with deletion percentage = 1.84% homopolymer indels = 43.42% >>>>>>> Coverage mean coverageData = 0.0314X std coverageData = 0.3356X There is a 2.8% of reference with a coverageData >= 1X There is a 0.23% 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 9365315 0.03757388833145575 0.6203545287334331 chr2 243199373 8003822 0.03291053715011017 0.4205926340135569 chr3 198022430 6265668 0.0316412034737681 0.1971560900787917 chr4 191154276 6102627 0.03192513988020859 0.205399446385428 chr5 180915260 5698971 0.03150077555646771 0.19335819926734726 chr6 171115067 5334046 0.03117227543732312 0.215583370697943 chr7 159138663 5194569 0.03264177857269041 0.3996549484934908 chr8 146364022 4881270 0.033350204054928195 0.4225561854582003 chr9 141213431 3949460 0.027968019557573102 0.29407872721038547 chr10 135534747 4543630 0.03352372805181833 0.4130012980492678 chr11 135006516 5201646 0.038528851451881035 0.36155649607256735 chr12 133851895 4194226 0.03133482719837474 0.19185343709845432 chr13 115169878 3493667 0.030334902325762643 0.18927403739236268 chr14 107349540 2751621 0.0256323501712257 0.1980622379977973 chr15 102531392 2702421 0.02635701073872088 0.17433111907447235 chr16 90354753 2233758 0.024722086285820514 0.19712993793264566 chr17 81195210 2892111 0.03561923172561534 0.24148905936637205 chr18 78077248 2580869 0.03305532746236138 0.5209416139841369 chr19 59128983 1890539 0.03197313574630566 0.4511372167319804 chr20 63025520 1894892 0.030065471891386218 0.1917959980556596 chr21 48129895 1262548 0.026232095457511387 0.19017900373112334 chr22 51304566 1012585 0.019736742339853338 0.15068530722908827 chrMT 16571 75922 4.581618490133366 4.567531022008659 chrX 155270560 5322406 0.034278268848904773 0.25424225426360186 chrY 59373566 269714 0.004542661291390178 0.11563091839851823