BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238523.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 = 3,919,547 number of mapped reads = 3,441,599 (87.81%) number of supplementary alignments = 29,833 (0.76%) number of secondary alignments = 0 number of mapped bases = 206,161,557 bp number of sequenced bases = 206,021,281 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,468,229 duplication rate = 24.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.4045 >>>>>>> ACTG content number of A's = 50,002,908 bp (24.27%) number of C's = 34,445,134 bp (16.72%) number of T's = 71,278,699 bp (34.6%) number of G's = 50,281,619 bp (24.41%) number of N's = 12,921 bp (0.01%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,347,757 number of insertions = 12,935 mapped reads with insertion percentage = 0.37% number of deletions = 83,125 mapped reads with deletion percentage = 2.39% homopolymer indels = 41.09% >>>>>>> Coverage mean coverageData = 0.0666X std coverageData = 1.017X There is a 2.05% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 24633862 0.09883169759484772 1.1811167177011643 chr2 243199373 18126894 0.07453511814769358 2.190319943214956 chr3 198022430 6830816 0.03449516299744428 0.7420006250274794 chr4 191154276 12930353 0.06764354567720997 0.6540068228781541 chr5 180915260 15590168 0.0861738694679487 0.7614664893848141 chr6 171115067 7575053 0.04426876681759415 0.8464751530522845 chr7 159138663 14151572 0.08892604558327853 0.8654009316474082 chr8 146364022 5631838 0.03847829489134973 0.6636742113410244 chr9 141213431 14952614 0.10588662773868868 0.8902896198175095 chr10 135534747 4978300 0.03673080232333337 0.6598079658567384 chr11 135006516 16116796 0.11937791210018338 1.0173426723327834 chr12 133851895 20083867 0.150045443884078 1.1136624306611598 chr13 115169878 1045609 0.009078840910120614 0.4756573445971831 chr14 107349540 1581661 0.01473374734535425 0.33159684946232143 chr15 102531392 1122916 0.010951923875177662 0.4978050639108333 chr16 90354753 4407029 0.048774733521766145 0.6097067422275577 chr17 81195210 4228402 0.0520769882853927 0.6177479235408918 chr18 78077248 14734848 0.1887214057544651 2.056236484660093 chr19 59128983 3318874 0.05612939427691493 0.8010692698992873 chr20 63025520 1023291 0.01623613736150055 0.2877304184892837 chr21 48129895 3004846 0.0624320082144372 0.6635131957749992 chr22 51304566 391214 0.007625325200100124 0.1783967647802646 chrMT 16571 288270 17.39605334620723 16.40462532177623 chrX 155270560 9065144 0.058382889840804336 0.6413446695641183 chrY 59373566 347320 0.005849741280488358 0.32685042298655625