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Detailed information for vg0327873390:

Variant ID: vg0327873390 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 27873390
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, G: 0.02, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

GCATCACTGGTAAATGTACAAAAATCACATCTTGTAAGCAAGTAAGGAGTATATGTTGTCACTACCGTTATACATACATACATACATACATACATACATA[C/T]
ATACATACATACATACATACATACATACATACATATATATATATATATATATATATATATATATATATATATAAACTTGATACGGAGTATATCATATAAC

Reverse complement sequence

GTTATATGATATACTCCGTATCAAGTTTATATATATATATATATATATATATATATATATATATATATGTATGTATGTATGTATGTATGTATGTATGTAT[G/A]
TATGTATGTATGTATGTATGTATGTATGTATAACGGTAGTGACAACATATACTCCTTACTTGCTTACAAGATGTGATTTTTGTACATTTACCAGTGATGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	29.80%	3.10%	18.32%	48.82%	NA
All Indica	2759	32.40%	4.70%	12.36%	50.49%	NA
All Japonica	1512	28.50%	0.10%	26.98%	44.44%	NA
Aus	269	0.40%	4.80%	28.25%	66.54%	NA
Indica I	595	52.80%	2.20%	4.87%	40.17%	NA
Indica II	465	41.30%	5.60%	12.04%	41.08%	NA
Indica III	913	18.50%	6.10%	15.88%	59.47%	NA
Indica Intermediate	786	28.00%	4.50%	14.12%	53.44%	NA
Temperate Japonica	767	40.70%	0.00%	32.86%	26.47%	NA
Tropical Japonica	504	13.90%	0.00%	17.86%	68.25%	NA
Japonica Intermediate	241	20.30%	0.40%	27.39%	51.87%	NA
VI/Aromatic	96	53.10%	0.00%	16.67%	30.21%	NA
Intermediate	90	33.30%	1.10%	27.78%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0327873390	C -> T	LOC_Os03g48940.1	upstream_gene_variant ; 1531.0bp to feature; MODIFIER	silent_mutation	Average:60.625; most accessible tissue: Callus, score: 75.334	N	N	N	N
vg0327873390	C -> T	LOC_Os03g48950.1	upstream_gene_variant ; 4553.0bp to feature; MODIFIER	silent_mutation	Average:60.625; most accessible tissue: Callus, score: 75.334	N	N	N	N
vg0327873390	C -> T	LOC_Os03g48940.2	upstream_gene_variant ; 1451.0bp to feature; MODIFIER	silent_mutation	Average:60.625; most accessible tissue: Callus, score: 75.334	N	N	N	N
vg0327873390	C -> T	LOC_Os03g48950.2	upstream_gene_variant ; 4553.0bp to feature; MODIFIER	silent_mutation	Average:60.625; most accessible tissue: Callus, score: 75.334	N	N	N	N
vg0327873390	C -> T	LOC_Os03g48940-LOC_Os03g48950	intergenic_region ; MODIFIER	silent_mutation	Average:60.625; most accessible tissue: Callus, score: 75.334	N	N	N	N
vg0327873390	C -> DEL	N	N	silent_mutation	Average:60.625; most accessible tissue: Callus, score: 75.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0327873390	9.93E-06	NA	mr1645	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
vg0327873390	NA	3.19E-06	mr1645	Ind_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
vg0327873390	1.19E-06	NA	mr1647	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
vg0327873390	NA	2.21E-10	mr1921	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