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Detailed information for vg0120050864:

Variant ID: vg0120050864 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 20050864
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TCAAAAATCCTCTAATCCGGATAAGGCCTTAAAAAGAGATAAATCCAATTTGGTCACTATGAAATCAGTTACAATTGGACTTGAACTCTCGAAATCGTCC[A/C]
TATTTCATCCTTGCGCTCAAATAAAGATGGTTTTGATGATGTGGCCTCATGTGGCAAAACAAAATTAACGAACATAGGTAGGATACAAGTACGAGAAGAA

Reverse complement sequence

TTCTTCTCGTACTTGTATCCTACCTATGTTCGTTAATTTTGTTTTGCCACATGAGGCCACATCATCAAAACCATCTTTATTTGAGCGCAAGGATGAAATA[T/G]
GGACGATTTCGAGAGTTCAAGTCCAATTGTAACTGATTTCATAGTGACCAAATTGGATTTATCTCTTTTTAAGGCCTTATCCGGATTAGAGGATTTTTGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.10%	11.30%	1.57%	0.00%	NA
All Indica	2759	97.90%	1.40%	0.62%	0.00%	NA
All Japonica	1512	67.10%	29.60%	3.31%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	98.10%	1.30%	0.65%	0.00%	NA
Indica III	913	97.40%	2.30%	0.33%	0.00%	NA
Indica Intermediate	786	97.20%	1.50%	1.27%	0.00%	NA
Temperate Japonica	767	90.20%	6.00%	3.78%	0.00%	NA
Tropical Japonica	504	26.20%	70.20%	3.57%	0.00%	NA
Japonica Intermediate	241	79.30%	19.50%	1.24%	0.00%	NA
VI/Aromatic	96	60.40%	37.50%	2.08%	0.00%	NA
Intermediate	90	81.10%	14.40%	4.44%	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
vg0120050864	A -> C	LOC_Os01g36229-LOC_Os01g36240	intergenic_region ; MODIFIER	silent_mutation	Average:54.953; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0120050864	NA	8.62E-07	mr1206	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
vg0120050864	NA	1.02E-06	mr1248	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
vg0120050864	NA	3.84E-10	mr1248	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
vg0120050864	NA	5.14E-08	mr1642	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
vg0120050864	NA	1.98E-11	mr1864	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
vg0120050864	NA	2.29E-06	mr1039_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
vg0120050864	4.64E-06	NA	mr1065_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
vg0120050864	6.75E-07	NA	mr1068_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
vg0120050864	3.06E-06	NA	mr1200_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