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Detailed information for vg0314830047:

Variant ID: vg0314830047 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14830047
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, G: 0.02, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

TCAGGATTTGAACTTAGTGAGTGAAGACATCTATCCACAACTCCACCGTAACAGCACGGTGTTTATAAGGACAAGTGATATTTCACTTGTTAGGGCTTTT[C/G]
ACAGTGTGATTAGGTGTCATTCTACCCCCAACGAGCTATGTCAAAGATTCTATGCCACGTCTGCGTCCCTCGTTACTCTGCGAAGTACGCGGATCCTAGT

Reverse complement sequence

ACTAGGATCCGCGTACTTCGCAGAGTAACGAGGGACGCAGACGTGGCATAGAATCTTTGACATAGCTCGTTGGGGGTAGAATGACACCTAATCACACTGT[G/C]
AAAAGCCCTAACAAGTGAAATATCACTTGTCCTTATAAACACCGTGCTGTTACGGTGGAGTTGTGGATAGATGTCTTCACTCACTAAGTTCAAATCCTGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.30%	47.40%	1.23%	0.08%	NA
All Indica	2759	28.40%	70.20%	1.27%	0.14%	NA
All Japonica	1512	85.70%	13.00%	1.26%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	53.60%	45.50%	0.67%	0.17%	NA
Indica II	465	40.60%	57.80%	1.08%	0.43%	NA
Indica III	913	11.10%	88.60%	0.33%	0.00%	NA
Indica Intermediate	786	22.30%	74.70%	2.93%	0.13%	NA
Temperate Japonica	767	96.50%	1.40%	2.09%	0.00%	NA
Tropical Japonica	504	76.40%	23.60%	0.00%	0.00%	NA
Japonica Intermediate	241	71.00%	27.80%	1.24%	0.00%	NA
VI/Aromatic	96	32.30%	66.70%	1.04%	0.00%	NA
Intermediate	90	52.20%	44.40%	3.33%	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
vg0314830047	C -> DEL	N	N	silent_mutation	Average:59.542; most accessible tissue: Callus, score: 82.142	N	N	N	N
vg0314830047	C -> G	LOC_Os03g25910.1	upstream_gene_variant ; 2209.0bp to feature; MODIFIER	silent_mutation	Average:59.542; most accessible tissue: Callus, score: 82.142	N	N	N	N
vg0314830047	C -> G	LOC_Os03g25900-LOC_Os03g25910	intergenic_region ; MODIFIER	silent_mutation	Average:59.542; most accessible tissue: Callus, score: 82.142	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314830047	NA	6.83E-06	mr1134	Jap_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
vg0314830047	NA	3.66E-06	mr1504	Jap_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
vg0314830047	5.39E-07	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
vg0314830047	1.18E-08	2.80E-10	mr1542	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
vg0314830047	3.00E-06	3.00E-06	mr1670	Jap_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
vg0314830047	5.25E-08	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
vg0314830047	8.68E-10	6.01E-12	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
vg0314830047	NA	7.32E-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