BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524725.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 = 1,381,340 number of mapped reads = 1,257,820 (91.06%) number of supplementary alignments = 4,627 (0.33%) number of secondary alignments = 0 number of mapped bases = 71,488,236 bp number of sequenced bases = 71,465,395 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,887 duplication rate = 3.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4902 >>>>>>> ACTG content number of A's = 17,191,001 bp (24.06%) number of C's = 12,993,657 bp (18.18%) number of T's = 23,424,259 bp (32.78%) number of G's = 17,848,206 bp (24.97%) number of N's = 8,272 bp (0.01%) GC percentage = 43.16% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 364,928 number of insertions = 5,678 mapped reads with insertion percentage = 0.45% number of deletions = 14,258 mapped reads with deletion percentage = 1.13% homopolymer indels = 40.51% >>>>>>> Coverage mean coverageData = 0.0231X std coverageData = 0.2239X There is a 2.07% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 5702967 0.022880452522523506 0.3113460355499677 chr2 243199373 6092079 0.025049731522128554 0.35745160277716653 chr3 198022430 4691939 0.02369397749537767 0.1720620816156513 chr4 191154276 4676401 0.024464014605668563 0.19700019224283213 chr5 180915260 4282635 0.023672049555134266 0.16831202988747446 chr6 171115067 3998502 0.023367328605843927 0.1829519621044603 chr7 159138663 3959124 0.024878454583974984 0.24925270215572984 chr8 146364022 3555405 0.02429152295363952 0.20930548619669903 chr9 141213431 3065212 0.021706235577549277 0.19132860433362384 chr10 135534747 3493087 0.025772630836873145 0.27784969057725944 chr11 135006516 3241925 0.02401310022695497 0.19697024978979008 chr12 133851895 3228923 0.024123102627721483 0.17241851938015682 chr13 115169878 2193124 0.019042513876762118 0.15174946686833854 chr14 107349540 2144663 0.019978315696555383 0.1581422883132871 chr15 102531392 2027935 0.019778674223012598 0.15619997584547232 chr16 90354753 2106295 0.023311391266821347 0.18185460472784587 chr17 81195210 2010997 0.02476743394099233 0.17806046051732552 chr18 78077248 1863602 0.023868694757274232 0.29110764528257654 chr19 59128983 1572673 0.026597328758385715 0.24853743070021378 chr20 63025520 1513146 0.024008465142374074 0.17949297702453101 chr21 48129895 933907 0.019403886087846232 0.17000527416240357 chr22 51304566 891611 0.017378784570558494 0.14584462427843795 chrMT 16571 16240 0.9800253454830729 1.2572236148890064 chrX 155270560 3973924 0.025593544584369375 0.18633429131565074 chrY 59373566 251920 0.004242965632214174 0.13377058097680533