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Detailed information for vg0314575945:

Variant ID: vg0314575945 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14575945
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.10, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

TATTGTCACGATTTCCCCCTTTGCAATGCCGTGGTGGTATTACGGGGCATGGCAACATGTGTGGAATCGTGTCTTGTGGGTACAGTGGTACACCTCTGGC[T/C]
AGAGTAAAACTATTCGAATAGCCGTGCCCGCGGTCATGGGCGAGTTGAGCAATGTTTTTCGTGATTAGTCCCATACTACTCAATAATGTTAATAATGTGA

Reverse complement sequence

TCACATTATTAACATTATTGAGTAGTATGGGACTAATCACGAAAAACATTGCTCAACTCGCCCATGACCGCGGGCACGGCTATTCGAATAGTTTTACTCT[A/G]
GCCAGAGGTGTACCACTGTACCCACAAGACACGATTCCACACATGTTGCCATGCCCCGTAATACCACCACGGCATTGCAAAGGGGGAAATCGTGACAATA

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	95.30%	1.40%	3.26%	0.00%	NA
All Indica	2759	92.50%	2.10%	5.40%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.13%	0.00%	NA
Aus	269	97.40%	2.20%	0.37%	0.00%	NA
Indica I	595	90.80%	2.40%	6.89%	0.00%	NA
Indica II	465	86.00%	3.90%	10.11%	0.00%	NA
Indica III	913	97.00%	0.90%	2.08%	0.00%	NA
Indica Intermediate	786	92.40%	2.30%	5.34%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	96.70%	2.20%	1.11%	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
vg0314575945	T -> C	LOC_Os03g25510.1	upstream_gene_variant ; 1170.0bp to feature; MODIFIER	silent_mutation	Average:56.288; most accessible tissue: Minghui63 flag leaf, score: 77.153	N	N	N	N
vg0314575945	T -> C	LOC_Os03g25530.1	upstream_gene_variant ; 2594.0bp to feature; MODIFIER	silent_mutation	Average:56.288; most accessible tissue: Minghui63 flag leaf, score: 77.153	N	N	N	N
vg0314575945	T -> C	LOC_Os03g25500.1	downstream_gene_variant ; 4182.0bp to feature; MODIFIER	silent_mutation	Average:56.288; most accessible tissue: Minghui63 flag leaf, score: 77.153	N	N	N	N
vg0314575945	T -> C	LOC_Os03g25510-LOC_Os03g25530	intergenic_region ; MODIFIER	silent_mutation	Average:56.288; most accessible tissue: Minghui63 flag leaf, score: 77.153	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314575945	8.57E-12	NA	mr1542	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
vg0314575945	4.72E-09	2.18E-15	mr1542	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
vg0314575945	8.98E-09	NA	mr1542_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
vg0314575945	4.26E-06	2.14E-16	mr1542_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