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Detailed information for vg0318167000:

Variant ID: vg0318167000 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 18167000
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACTTATCCCGTGCGCCTCCTCCTCCTCCTCGATGTTGCGCGCACGCCTCATCCTCTCCGCGCATGCGGATCTTTTTTTTCCTGGTTGTTTAACAACCGG[A/G]
ACTAGAAATAGCTCTTTAGTCCAACCGGGATTAAAGGTAAAGGAGGGGTCTGACACCGCCTACCTTTTTTGAACTAGGATTAAAGATTAAAAAGTAGCTC

Reverse complement sequence

GAGCTACTTTTTAATCTTTAATCCTAGTTCAAAAAAGGTAGGCGGTGTCAGACCCCTCCTTTACCTTTAATCCCGGTTGGACTAAAGAGCTATTTCTAGT[T/C]
CCGGTTGTTAAACAACCAGGAAAAAAAAGATCCGCATGCGCGGAGAGGATGAGGCGTGCGCGCAACATCGAGGAGGAGGAGGAGGCGCACGGGATAAGTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.40%	15.70%	1.95%	0.00%	NA
All Indica	2759	99.30%	0.40%	0.33%	0.00%	NA
All Japonica	1512	47.80%	47.30%	4.89%	0.00%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	97.80%	1.30%	0.86%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.40%	0.51%	0.00%	NA
Temperate Japonica	767	12.50%	81.70%	5.74%	0.00%	NA
Tropical Japonica	504	88.50%	8.30%	3.17%	0.00%	NA
Japonica Intermediate	241	75.10%	19.10%	5.81%	0.00%	NA
VI/Aromatic	96	93.80%	2.10%	4.17%	0.00%	NA
Intermediate	90	81.10%	15.60%	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
vg0318167000	A -> G	LOC_Os03g31760.1	3_prime_UTR_variant ; 258.0bp to feature; MODIFIER	silent_mutation	Average:76.525; most accessible tissue: Zhenshan97 panicle, score: 88.888	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0318167000	NA	1.55E-12	mr1031	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
vg0318167000	NA	6.59E-13	mr1056	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
vg0318167000	NA	7.01E-06	mr1521	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
vg0318167000	NA	3.75E-06	mr1577	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
vg0318167000	NA	5.40E-07	mr1587	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
vg0318167000	NA	1.37E-07	mr1723	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
vg0318167000	NA	2.51E-06	mr1844	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
vg0318167000	NA	1.39E-11	mr1902	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
vg0318167000	NA	2.41E-09	mr1486_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
vg0318167000	2.39E-06	1.22E-08	mr1577_2	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
vg0318167000	NA	7.08E-07	mr1629_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
vg0318167000	NA	4.73E-07	mr1792_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
vg0318167000	1.28E-06	NA	mr1803_2	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