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Detailed information for vg0318126392:

Variant ID: vg0318126392 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 18126392
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.07, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAACTAGTCTCAAATTTTCAAATTTATTTTTGCATACGGCTTCTTAAGTTACCCGTATGGAAAAATTGATTTTTCCATGTGGGTCCTTAAGTGGTCCA[C/T]
GTACAAACAAATGAAAAAAATTCAATTCTGAAAAATAATCACTCGAATTTTTAAAAACTTTCAATTGAAATGTTCAACCCAAAATTTAAAATATTCAACC

Reverse complement sequence

GGTTGAATATTTTAAATTTTGGGTTGAACATTTCAATTGAAAGTTTTTAAAAATTCGAGTGATTATTTTTCAGAATTGAATTTTTTTCATTTGTTTGTAC[G/A]
TGGACCACTTAAGGACCCACATGGAAAAATCAATTTTTCCATACGGGTAACTTAAGAAGCCGTATGCAAAAATAAATTTGAAAATTTGAGACTAGTTTAT

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	55.60%	31.10%	10.75%	2.48%	NA
All Indica	2759	76.40%	2.50%	17.14%	3.95%	NA
All Japonica	1512	14.30%	84.10%	1.52%	0.13%	NA
Aus	269	90.30%	7.10%	1.49%	1.12%	NA
Indica I	595	83.90%	2.40%	8.74%	5.04%	NA
Indica II	465	64.70%	3.40%	26.45%	5.38%	NA
Indica III	913	80.00%	1.20%	16.10%	2.74%	NA
Indica Intermediate	786	73.70%	3.40%	19.21%	3.69%	NA
Temperate Japonica	767	0.10%	99.70%	0.00%	0.13%	NA
Tropical Japonica	504	39.10%	60.30%	0.40%	0.20%	NA
Japonica Intermediate	241	7.50%	83.80%	8.71%	0.00%	NA
VI/Aromatic	96	22.90%	76.00%	0.00%	1.04%	NA
Intermediate	90	43.30%	45.60%	8.89%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0318126392	C -> T	LOC_Os03g31730.1	intron_variant ; MODIFIER	silent_mutation	Average:17.541; most accessible tissue: Callus, score: 27.038	N	N	N	N
vg0318126392	C -> DEL	N	N	silent_mutation	Average:17.541; most accessible tissue: Callus, score: 27.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0318126392	NA	8.70E-10	mr1198	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
vg0318126392	NA	6.26E-07	mr1215	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
vg0318126392	NA	8.48E-08	mr1217	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
vg0318126392	NA	8.49E-15	mr1218	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
vg0318126392	NA	5.97E-09	mr1275	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
vg0318126392	NA	5.85E-10	mr1307	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
vg0318126392	NA	2.85E-09	mr1352	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
vg0318126392	NA	3.36E-06	mr1450	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
vg0318126392	NA	7.34E-09	mr1575	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
vg0318126392	4.04E-07	1.40E-13	mr1750	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
vg0318126392	NA	7.54E-07	mr1830	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
vg0318126392	NA	6.94E-07	mr1845	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
vg0318126392	NA	8.26E-07	mr1850	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
vg0318126392	NA	1.41E-08	mr1852	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
vg0318126392	6.56E-08	6.55E-08	mr1987	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
vg0318126392	NA	5.83E-09	mr1136_2	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
vg0318126392	NA	7.06E-16	mr1750_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
vg0318126392	NA	1.83E-08	mr1800_2	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
vg0318126392	NA	7.09E-08	mr1987_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