BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716972.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 = 3,310,217 number of mapped reads = 2,554,719 (77.18%) number of supplementary alignments = 13,043 (0.39%) number of secondary alignments = 0 number of mapped bases = 145,789,309 bp number of sequenced bases = 145,746,578 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,720 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3672 >>>>>>> ACTG content number of A's = 37,759,951 bp (25.91%) number of C's = 26,636,244 bp (18.28%) number of T's = 45,273,170 bp (31.06%) number of G's = 36,074,869 bp (24.75%) number of N's = 2,344 bp (0%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 718,546 number of insertions = 8,584 mapped reads with insertion percentage = 0.33% number of deletions = 27,241 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.66% >>>>>>> Coverage mean coverageData = 0.0471X std coverageData = 0.4116X There is a 4.06% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% 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 0.01% 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 12436144 0.049894134466369096 0.5082610389683339 chr2 243199373 13482309 0.05543726874657691 0.4906742585485784 chr3 198022430 11446159 0.05780233582630008 0.30197709064088957 chr4 191154276 8565699 0.044810397021932166 0.2512745666996879 chr5 180915260 7722866 0.042687753371385036 0.23256434975136836 chr6 171115067 8429241 0.04926065920308467 0.2922789434656499 chr7 159138663 9296499 0.058417601510199944 1.0506938263637764 chr8 146364022 10489407 0.07166656707479656 0.38756920494123975 chr9 141213431 5067656 0.03588650147591131 0.2736654786949302 chr10 135534747 6978802 0.05149086971771158 0.5221217142479618 chr11 135006516 4399088 0.03258426430321334 0.27369805337603176 chr12 133851895 7080867 0.05290076020216225 0.28426455504310366 chr13 115169878 4017747 0.03488539772526285 0.20798018704279628 chr14 107349540 3971768 0.036998463151309266 0.22533893482444578 chr15 102531392 3533411 0.03446174806638732 0.21530824743888763 chr16 90354753 4353057 0.04817739914578705 0.2705007632901268 chr17 81195210 5467618 0.067339169391889 0.30772618212298214 chr18 78077248 3633639 0.046539025043505634 0.4752120717683356 chr19 59128983 2909449 0.049205125006124326 0.4684868041390346 chr20 63025520 3257614 0.051687221303370445 0.26662991860474977 chr21 48129895 1461323 0.030362064990999877 0.20239831433146516 chr22 51304566 2045849 0.03987654821989918 0.22802276985887243 chrMT 16571 32401 1.9552833262929215 1.935504048164492 chrX 155270560 5395470 0.03474882811010664 0.25865930114526325 chrY 59373566 315226 0.00530919769919159 0.11702544439370281