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Detailed information for vg0203433301:

Variant ID: vg0203433301 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3433301
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.06, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCTTAATTTAATTAACTTAAAATATAAAAAAGTACATCACACAATTTAGTGATATAAAAAAAGAATACTTAAAAGCACATGGCAAAATGCAGGGACAA[T/C]
AAGCTCACACTGAGAACTCGACAATTGATCTGGTGGACAAAATTAGAGCTGATGAAGAAGAACACAGAGATCAGGTTGTGGCCACAGAACCCCAGATGCA

Reverse complement sequence

TGCATCTGGGGTTCTGTGGCCACAACCTGATCTCTGTGTTCTTCTTCATCAGCTCTAATTTTGTCCACCAGATCAATTGTCGAGTTCTCAGTGTGAGCTT[A/G]
TTGTCCCTGCATTTTGCCATGTGCTTTTAAGTATTCTTTTTTTATATCACTAAATTGTGTGATGTACTTTTTTATATTTTAAGTTAATTAAATTAAGAAA

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	64.70%	19.00%	0.55%	15.76%	NA
All Indica	2759	92.40%	1.30%	0.62%	5.73%	NA
All Japonica	1512	14.70%	54.70%	0.33%	30.22%	NA
Aus	269	85.10%	5.20%	0.37%	9.29%	NA
Indica I	595	94.50%	2.70%	0.50%	2.35%	NA
Indica II	465	91.20%	0.00%	0.22%	8.60%	NA
Indica III	913	95.40%	0.40%	0.44%	3.72%	NA
Indica Intermediate	786	87.90%	2.00%	1.15%	8.91%	NA
Temperate Japonica	767	5.30%	67.40%	0.13%	27.12%	NA
Tropical Japonica	504	23.20%	44.80%	0.60%	31.35%	NA
Japonica Intermediate	241	27.00%	34.90%	0.41%	37.76%	NA
VI/Aromatic	96	15.60%	2.10%	2.08%	80.21%	NA
Intermediate	90	46.70%	21.10%	1.11%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0203433301	T -> DEL	N	N	silent_mutation	Average:26.129; most accessible tissue: Callus, score: 79.861	N	N	N	N
vg0203433301	T -> C	LOC_Os02g06790.1	upstream_gene_variant ; 2226.0bp to feature; MODIFIER	silent_mutation	Average:26.129; most accessible tissue: Callus, score: 79.861	N	N	N	N
vg0203433301	T -> C	LOC_Os02g06810.1	downstream_gene_variant ; 1014.0bp to feature; MODIFIER	silent_mutation	Average:26.129; most accessible tissue: Callus, score: 79.861	N	N	N	N
vg0203433301	T -> C	LOC_Os02g06790-LOC_Os02g06810	intergenic_region ; MODIFIER	silent_mutation	Average:26.129; most accessible tissue: Callus, score: 79.861	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203433301	NA	6.61E-07	mr1113	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
vg0203433301	NA	4.29E-07	mr1114	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
vg0203433301	NA	5.31E-06	mr1116	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
vg0203433301	NA	1.28E-06	mr1117	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
vg0203433301	NA	2.15E-15	mr1276	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
vg0203433301	NA	6.99E-10	mr1945	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
vg0203433301	NA	3.31E-06	mr1114_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
vg0203433301	NA	9.67E-06	mr1119_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
vg0203433301	NA	1.35E-12	mr1258_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
vg0203433301	NA	1.93E-06	mr1267_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
vg0203433301	NA	6.92E-06	mr1648_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
vg0203433301	7.60E-06	7.61E-06	mr1655_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
vg0203433301	1.94E-06	1.94E-06	mr1669_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
vg0203433301	NA	1.26E-06	mr1861_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
vg0203433301	NA	7.21E-06	mr1977_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
vg0203433301	4.22E-07	2.93E-18	mr1980_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
vg0203433301	NA	2.61E-06	mr1980_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