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Detailed information for vg0620184702:

Variant ID: vg0620184702 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20184702
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.60, C: 0.40, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

GGTAACATCAACCGGGACTAAAGATCCCCTCTCTTTAGTCCCGGTTGGTGGTAACAACCGCATAACCGGGACTAAAGACGTCCATCTTTAGTCCCGGATC[T/C]
TTACTCCCGGTTGGAAAACCAGGATTAAAGGGGGTTCCCAACCGGGAGTAAAGATGGTTTCACCACCAGTGGATCTTATGAACATACACACACTCTACCT

Reverse complement sequence

AGGTAGAGTGTGTGTATGTTCATAAGATCCACTGGTGGTGAAACCATCTTTACTCCCGGTTGGGAACCCCCTTTAATCCTGGTTTTCCAACCGGGAGTAA[A/G]
GATCCGGGACTAAAGATGGACGTCTTTAGTCCCGGTTATGCGGTTGTTACCACCAACCGGGACTAAAGAGAGGGGATCTTTAGTCCCGGTTGATGTTACC

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	58.00%	41.70%	0.34%	0.00%	NA
All Indica	2759	81.40%	18.30%	0.36%	0.00%	NA
All Japonica	1512	8.10%	91.70%	0.26%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	81.50%	18.30%	0.17%	0.00%	NA
Indica II	465	80.00%	19.80%	0.22%	0.00%	NA
Indica III	913	80.00%	19.50%	0.55%	0.00%	NA
Indica Intermediate	786	83.70%	15.90%	0.38%	0.00%	NA
Temperate Japonica	767	6.80%	93.10%	0.13%	0.00%	NA
Tropical Japonica	504	7.10%	92.70%	0.20%	0.00%	NA
Japonica Intermediate	241	14.10%	85.10%	0.83%	0.00%	NA
VI/Aromatic	96	66.70%	33.30%	0.00%	0.00%	NA
Intermediate	90	45.60%	52.20%	2.22%	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
vg0620184702	T -> C	LOC_Os06g34730-LOC_Os06g34750	intergenic_region ; MODIFIER	silent_mutation	Average:52.821; most accessible tissue: Minghui63 root, score: 68.826	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620184702	NA	8.29E-06	mr1536	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
vg0620184702	1.58E-06	1.58E-06	mr1497_2	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
vg0620184702	NA	9.78E-06	mr1536_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