BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238488.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,314,696 number of mapped reads = 3,910,229 (90.63%) number of supplementary alignments = 27,197 (0.63%) number of secondary alignments = 0 number of mapped bases = 238,335,284 bp number of sequenced bases = 238,204,972 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 918,785 duplication rate = 18.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0605 >>>>>>> ACTG content number of A's = 57,716,245 bp (24.23%) number of C's = 41,643,480 bp (17.48%) number of T's = 80,130,035 bp (33.64%) number of G's = 58,699,375 bp (24.64%) number of N's = 15,837 bp (0.01%) GC percentage = 42.12% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,501,766 number of insertions = 16,767 mapped reads with insertion percentage = 0.42% number of deletions = 75,044 mapped reads with deletion percentage = 1.9% homopolymer indels = 41.28% >>>>>>> Coverage mean coverageData = 0.077X std coverageData = 0.9378X There is a 4.36% of reference with a coverageData >= 1X There is a 1.71% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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% 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 24074418 0.09658719365838611 1.1251744953827918 chr2 243199373 15246039 0.0626894667199656 2.040880420011489 chr3 198022430 15854950 0.08006643489830925 0.4627420634110354 chr4 191154276 13986041 0.07316624714165432 0.4862836034206933 chr5 180915260 17422066 0.0962995935224038 0.5121897417235911 chr6 171115067 9461065 0.05529066005625326 0.7744174672139157 chr7 159138663 12899177 0.08105621070851902 0.8299872125393616 chr8 146364022 5192532 0.03547683323433132 1.0071541084269242 chr9 141213431 17413552 0.12331370944453576 0.9290938248062363 chr10 135534747 11067674 0.08165931058254751 0.7785853660337543 chr11 135006516 8408018 0.06227860883396176 0.5034477716864793 chr12 133851895 15240009 0.11385725245055366 0.5895023433928618 chr13 115169878 6729842 0.05843404644398425 0.5463314178291182 chr14 107349540 1955314 0.01821446090966016 0.3473051152827549 chr15 102531392 12488539 0.12180210135057953 0.6607782464882552 chr16 90354753 10025585 0.11095802563922674 0.6788061968797251 chr17 81195210 8990939 0.11073238187326567 0.5847319865173193 chr18 78077248 5585717 0.07154090523272541 2.029869657831272 chr19 59128983 6146179 0.1039452851742774 0.9210131653415751 chr20 63025520 7927987 0.12579010851477307 0.6106324442039424 chr21 48129895 4761494 0.0989300724632788 0.5780895497903736 chr22 51304566 3361184 0.06551432478738832 0.4167917921536392 chrMT 16571 4852 0.2928006758795486 0.6507461781796728 chrX 155270560 3397722 0.021882589977134107 0.3296536968516477 chrY 59373566 694389 0.011695255090455573 0.44684458270330873