BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708540.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 24,013,773 number of mapped reads = 23,167,785 (96.48%) number of supplementary alignments = 523 (0%) number of secondary alignments = 0 number of mapped bases = 1,155,324,581 bp number of sequenced bases = 1,155,222,704 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 213,431 duplication rate = 0.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5745 >>>>>>> ACTG content number of A's = 361,141,186 bp (31.26%) number of C's = 215,257,403 bp (18.63%) number of T's = 359,309,278 bp (31.1%) number of G's = 219,055,032 bp (18.96%) number of N's = 459,805 bp (0.04%) GC percentage = 37.6% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 3,986,038 number of insertions = 64,178 mapped reads with insertion percentage = 0.28% number of deletions = 61,421 mapped reads with deletion percentage = 0.26% homopolymer indels = 48.25% >>>>>>> Coverage mean coverageData = 0.3732X std coverageData = 0.6829X There is a 28.31% of reference with a coverageData >= 1X There is a 7.05% of reference with a coverageData >= 2X There is a 1.55% of reference with a coverageData >= 3X There is a 0.32% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.01% 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 88100960 0.35346335205319307 0.6792417775018325 chr2 243199373 107046360 0.44015886504773183 0.7259294336253168 chr3 198022430 89873988 0.4538576160286489 0.7320107550137943 chr4 191154276 97892967 0.512114973561983 0.7763087224035258 chr5 180915260 83315221 0.4605206935003714 0.7392097983494686 chr6 171115067 78794654 0.46047759195863214 0.74268332054465 chr7 159138663 66428800 0.41742715910589245 0.7181738388342934 chr8 146364022 64609048 0.44142711519638345 0.7262308672972682 chr9 141213431 47962950 0.3396486414950147 0.6587972919691704 chr10 135534747 48939331 0.36108327999461276 0.6562927561300581 chr11 135006516 51300285 0.3799837705611187 0.6932291681630799 chr12 133851895 53427986 0.3991574867132064 0.702765534925068 chr13 115169878 49473102 0.4295663315715243 0.7346315195903316 chr14 107349540 36811246 0.3429101419531001 0.6618952213886645 chr15 102531392 30631772 0.2987550583532505 0.6210398029185381 chr16 90354753 20273104 0.22437230280514409 0.5298591928120575 chr17 81195210 17934196 0.22087751235571654 0.5335869471165435 chr18 78077248 35140024 0.4500673999165544 0.733961860712602 chr19 59128983 7716973 0.1305108359465611 0.39394401213101143 chr20 63025520 17147488 0.27207213839727146 0.5840612739491331 chr21 48129895 15007335 0.3118090118418085 0.6545330777456128 chr22 51304566 5532741 0.10784110326554561 0.3651349807637054 chrMT 16571 1027 0.061975740751915996 0.2489918013898483 chrX 155270560 36752093 0.23669711115874123 0.5128309759227018 chrY 59373566 5210930 0.08776515124592651 0.3336635838839876