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Detailed information for vg0139380327:

Variant ID: vg0139380327 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 39380327
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

CACCCACCATGGGGCGATCAACACAGACAATCAACGGCCTCAATCAACACCCAACACAATACATGGGAGAACATACAAGCCTACATACGCCAAGACAAGC[C/T]
GCCGGATATCGACTTCAGGGATAGGCACAGCTAGTCTCCTACGGTGTCTCCAGATACAGTCAGGAGAGACGAAAGCGCTATCTCTGATCTCGCCGGGCAC

Reverse complement sequence

GTGCCCGGCGAGATCAGAGATAGCGCTTTCGTCTCTCCTGACTGTATCTGGAGACACCGTAGGAGACTAGCTGTGCCTATCCCTGAAGTCGATATCCGGC[G/A]
GCTTGTCTTGGCGTATGTAGGCTTGTATGTTCTCCCATGTATTGTGTTGGGTGTTGATTGAGGCCGTTGATTGTCTGTGTTGATCGCCCCATGGTGGGTG

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	69.30%	22.30%	7.85%	0.59%	NA
All Indica	2759	61.70%	31.90%	5.40%	1.01%	NA
All Japonica	1512	95.40%	4.00%	0.60%	0.00%	NA
Aus	269	9.70%	31.60%	58.74%	0.00%	NA
Indica I	595	37.10%	53.40%	7.56%	1.85%	NA
Indica II	465	89.20%	9.90%	0.65%	0.22%	NA
Indica III	913	56.30%	35.20%	7.23%	1.31%	NA
Indica Intermediate	786	70.10%	24.90%	4.45%	0.51%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	87.90%	10.90%	1.19%	0.00%	NA
Japonica Intermediate	241	97.10%	1.70%	1.24%	0.00%	NA
VI/Aromatic	96	32.30%	17.70%	50.00%	0.00%	NA
Intermediate	90	83.30%	8.90%	7.78%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0139380327	C -> T	LOC_Os01g67750.1	upstream_gene_variant ; 759.0bp to feature; MODIFIER	silent_mutation	Average:23.475; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0139380327	C -> T	LOC_Os01g67760.1	upstream_gene_variant ; 1301.0bp to feature; MODIFIER	silent_mutation	Average:23.475; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0139380327	C -> T	LOC_Os01g67750-LOC_Os01g67760	intergenic_region ; MODIFIER	silent_mutation	Average:23.475; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0139380327	C -> DEL	N	N	silent_mutation	Average:23.475; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0139380327	2.14E-06	NA	mr1047_2	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
vg0139380327	NA	2.55E-07	mr1191_2	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
vg0139380327	NA	5.08E-07	mr1662_2	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