BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819027.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 597,218 number of mapped reads = 535,031 (89.59%) number of supplementary alignments = 2,346 (0.39%) number of secondary alignments = 0 number of mapped bases = 30,380,645 bp number of sequenced bases = 30,372,357 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,561 duplication rate = 1.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8114 >>>>>>> ACTG content number of A's = 7,683,549 bp (25.3%) number of C's = 5,864,104 bp (19.31%) number of T's = 9,525,860 bp (31.36%) number of G's = 7,298,171 bp (24.03%) number of N's = 673 bp (0%) GC percentage = 43.34% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 148,836 number of insertions = 2,240 mapped reads with insertion percentage = 0.42% number of deletions = 4,992 mapped reads with deletion percentage = 0.93% homopolymer indels = 41.23% >>>>>>> Coverage mean coverageData = 0.0098X std coverageData = 0.1121X There is a 0.94% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 3398455 0.013634690202035645 0.14899208818491724 chr2 243199373 2549442 0.010482929986830189 0.12316060371909722 chr3 198022430 1988302 0.010040791843631047 0.10324209637931916 chr4 191154276 1937111 0.010133757091575603 0.10732232145553276 chr5 180915260 1509728 0.008344945583915917 0.0946656897520067 chr6 171115067 1590398 0.009294318892444463 0.10118395485632782 chr7 159138663 1325930 0.00833191617300442 0.10311463646990131 chr8 146364022 1924772 0.013150581500144892 0.12404522731895823 chr9 141213431 1131974 0.008016050541254819 0.10642062921399212 chr10 135534747 1460102 0.010772897963944258 0.12332636814308198 chr11 135006516 944529 0.006996173429140265 0.09670655188173766 chr12 133851895 1358492 0.010149217536292632 0.10414775762510922 chr13 115169878 940918 0.008169827183458508 0.09284027752283572 chr14 107349540 1065520 0.009925706248950858 0.1062558211279892 chr15 102531392 867344 0.008459301908238992 0.09477023809866321 chr16 90354753 918180 0.010161944662722945 0.10736293760758633 chr17 81195210 682061 0.008400261542522028 0.09538317847130115 chr18 78077248 740661 0.009486259044376154 0.15815542117372294 chr19 59128983 581357 0.00983201419175432 0.11971598554934587 chr20 63025520 929301 0.014744836694723026 0.12669689909575746 chr21 48129895 394506 0.008196693551897423 0.09614277160221978 chr22 51304566 370567 0.007222885386068757 0.08751708228625321 chrMT 16571 1649 0.09951119425502383 0.34399650766954876 chrX 155270560 1680902 0.0108256323671403 0.11322059053232217 chrY 59373566 88444 0.0014896191345488664 0.04809985203187882