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Detailed information for vg0504420610:

Variant ID: vg0504420610 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 4420610
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

CCAAAATGTGTATGGTTTAATCATGATAGCACATTTTTGGCTCTGGCAGGAATTTATATAAAATGCGGAACTTTCAATTTTATCATTTTGAAAAACAAAA[T/C]
ATCCGGAATTCAGGTCAAACTAGTATCAGGATCATAGCAACTCATATTTACTATCTCATATCTCGCAACAACTTAGACTTAGATCAGCAAGTACAGCTCA

Reverse complement sequence

TGAGCTGTACTTGCTGATCTAAGTCTAAGTTGTTGCGAGATATGAGATAGTAAATATGAGTTGCTATGATCCTGATACTAGTTTGACCTGAATTCCGGAT[A/G]
TTTTGTTTTTCAAAATGATAAAATTGAAAGTTCCGCATTTTATATAAATTCCTGCCAGAGCCAAAAATGTGCTATCATGATTAAACCATACACATTTTGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	43.90%	15.80%	34.15%	6.18%	NA
All Indica	2759	6.60%	26.40%	57.09%	9.93%	NA
All Japonica	1512	98.80%	0.10%	0.66%	0.46%	NA
Aus	269	91.10%	3.30%	2.97%	2.60%	NA
Indica I	595	6.40%	23.40%	58.66%	11.60%	NA
Indica II	465	7.10%	22.20%	58.49%	12.26%	NA
Indica III	913	2.80%	33.60%	55.64%	7.89%	NA
Indica Intermediate	786	10.90%	22.60%	56.74%	9.67%	NA
Temperate Japonica	767	98.30%	0.00%	0.78%	0.91%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	94.80%	1.00%	3.12%	1.04%	NA
Intermediate	90	66.70%	10.00%	20.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0504420610	T -> DEL	N	N	silent_mutation	Average:7.67; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0504420610	T -> C	LOC_Os05g08110.1	upstream_gene_variant ; 3889.0bp to feature; MODIFIER	silent_mutation	Average:7.67; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0504420610	T -> C	LOC_Os05g08120.1	downstream_gene_variant ; 746.0bp to feature; MODIFIER	silent_mutation	Average:7.67; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0504420610	T -> C	LOC_Os05g08110-LOC_Os05g08120	intergenic_region ; MODIFIER	silent_mutation	Average:7.67; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0504420610	NA	8.15E-31	mr1257	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0504420610	8.00E-07	2.32E-07	mr1961	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0504420610	NA	5.95E-36	mr1129_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251