BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524755.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 = 2,787,844 number of mapped reads = 2,535,460 (90.95%) number of supplementary alignments = 10,530 (0.38%) number of secondary alignments = 0 number of mapped bases = 146,609,767 bp number of sequenced bases = 146,558,855 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 131,944 duplication rate = 3.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1602 >>>>>>> ACTG content number of A's = 36,376,741 bp (24.82%) number of C's = 28,948,750 bp (19.75%) number of T's = 48,222,038 bp (32.9%) number of G's = 33,008,490 bp (22.52%) number of N's = 2,836 bp (0%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 757,805 number of insertions = 9,595 mapped reads with insertion percentage = 0.38% number of deletions = 32,060 mapped reads with deletion percentage = 1.26% homopolymer indels = 43.64% >>>>>>> Coverage mean coverageData = 0.0474X std coverageData = 0.443X There is a 4.11% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.07% 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 15717276 0.06305812172881206 0.8646665395984805 chr2 243199373 11999629 0.04934070697624701 0.600444307461955 chr3 198022430 12433416 0.06278791751015277 0.2827240953287691 chr4 191154276 8318970 0.04351966471312418 0.25997438774877013 chr5 180915260 6594018 0.03644810283002108 0.21582549487001118 chr6 171115067 9018495 0.05270427179857867 0.30304869764779413 chr7 159138663 10625784 0.0667705999264302 0.7695686504215079 chr8 146364022 8257419 0.056416999800675056 0.44037022988685837 chr9 141213431 4815906 0.03410373904164966 0.3080423806419802 chr10 135534747 7618092 0.05620766754373327 0.4232191303055192 chr11 135006516 6630297 0.04911094068970715 0.3412217627805641 chr12 133851895 6508721 0.048626289526943194 0.25457977497449097 chr13 115169878 4499306 0.03906669068452082 0.22612760133040774 chr14 107349540 5367207 0.04999748485182144 0.2622506503399753 chr15 102531392 3843597 0.03748702641235964 0.223676477249495 chr16 90354753 3637395 0.040256819693812895 0.2575668982349929 chr17 81195210 3327610 0.0409828363027819 0.23617083668621633 chr18 78077248 3032751 0.03884295460823619 0.5911979019269312 chr19 59128983 2475450 0.041865255825556814 0.5680110182805255 chr20 63025520 2578099 0.04090563632001767 0.23420742827208507 chr21 48129895 1846014 0.03835483123326988 0.2513442893862412 chr22 51304566 1259017 0.0245400575067724 0.17592790552629178 chrMT 16571 8274 0.4993060165349104 0.7845877506808944 chrX 155270560 5781063 0.0372321900558612 0.24480546850324583 chrY 59373566 415961 0.007005828149180058 0.21731909624392526