BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549067.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,297,281 number of mapped reads = 8,885,924 (86.29%) number of secondary alignments = 0 number of mapped bases = 352,941,395 bp number of sequenced bases = 352,907,711 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 355,822 duplication rate = 2.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7594 >>>>>>> ACTG content number of A's = 105,625,932 bp (29.93%) number of C's = 70,965,040 bp (20.11%) number of T's = 105,688,549 bp (29.95%) number of G's = 70,621,554 bp (20.01%) number of N's = 6,636 bp (0%) GC percentage = 40.12% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,096,298 number of insertions = 8,617 mapped reads with insertion percentage = 0.1% number of deletions = 26,671 mapped reads with deletion percentage = 0.3% homopolymer indels = 44.41% >>>>>>> Coverage mean coverageData = 0.114X std coverageData = 1.1497X There is a 9.42% of reference with a coverageData >= 1X There is a 1.43% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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% 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 28370740 0.11382414970994195 2.842492209566917 chr2 243199373 30863663 0.1269068362277398 0.6819732415094635 chr3 198022430 25253187 0.12752690187672175 0.4176605634926137 chr4 191154276 25434601 0.13305797564266886 0.4466300934675837 chr5 180915260 23235743 0.12843440072440546 0.4284994432842848 chr6 171115067 21477988 0.12551780726591422 0.5552175568353714 chr7 159138663 20003296 0.12569727320129614 1.0113351551001593 chr8 146364022 18948085 0.1294586247431763 2.3633294528056203 chr9 141213431 14835246 0.10505548866665523 0.638200545504901 chr10 135534747 16795264 0.12391851072699461 0.862673849061145 chr11 135006516 16265031 0.1204758961411907 0.6478410599557652 chr12 133851895 16274663 0.12158709445241699 0.4441041200996795 chr13 115169878 12194140 0.10587959466276417 0.36636130386413995 chr14 107349540 11091691 0.10332313487323747 0.4424063115552588 chr15 102531392 9776110 0.09534748148157396 0.3502905219362425 chr16 90354753 9049161 0.10015146629862405 0.48690343414130705 chr17 81195210 8013210 0.09869067399419251 0.4239502681373184 chr18 78077248 9718772 0.12447636474072447 1.4169357410967136 chr19 59128983 5762904 0.09746326940884473 2.129702521011885 chr20 63025520 6819632 0.10820429565674348 0.4063847795716674 chr21 48129895 4569836 0.09494797360351606 0.43884820760299104 chr22 51304566 3149865 0.061395412642219795 0.3351738744735298 chrMT 16571 39614 2.3905618248747813 2.8196478887510796 chrX 155270560 11955446 0.07699750680360784 0.463395097471165 chrY 59373566 3043507 0.05126030328041944 0.49842977656006743