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Detailed information for vg0812490623:

Variant ID: vg0812490623 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12490623
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTGACTGCCCTCACCGGTAGCAGCGCTTCTCCTGGTTGTCACCATCTGAAAATCCCTCACAGAACCAGCAAACAGAGAGAGCTGACTATTAAAACTAAC[C/T]
ACCCACGACTACCATAATTCTTGAATTTATTTCTATTATTAAATTGGTTCATTAAGGTTCAAGTTGCTTATGCAAATAAAATAAAGACAGGCTCCGACAC

Reverse complement sequence

GTGTCGGAGCCTGTCTTTATTTTATTTGCATAAGCAACTTGAACCTTAATGAACCAATTTAATAATAGAAATAAATTCAAGAATTATGGTAGTCGTGGGT[G/A]
GTTAGTTTTAATAGTCAGCTCTCTCTGTTTGCTGGTTCTGTGAGGGATTTTCAGATGGTGACAACCAGGAGAAGCGCTGCTACCGGTGAGGGCAGTCACC

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	89.00%	10.90%	0.06%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	72.40%	27.50%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	97.70%	2.30%	0.00%	0.00%	NA
Tropical Japonica	504	44.00%	55.80%	0.20%	0.00%	NA
Japonica Intermediate	241	51.50%	48.50%	0.00%	0.00%	NA
VI/Aromatic	96	16.70%	81.20%	2.08%	0.00%	NA
Intermediate	90	78.90%	21.10%	0.00%	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
vg0812490623	C -> T	LOC_Os08g20790.1	upstream_gene_variant ; 1912.0bp to feature; MODIFIER	silent_mutation	Average:50.194; most accessible tissue: Minghui63 flag leaf, score: 74.161	N	N	N	N
vg0812490623	C -> T	LOC_Os08g20820.1	downstream_gene_variant ; 4631.0bp to feature; MODIFIER	silent_mutation	Average:50.194; most accessible tissue: Minghui63 flag leaf, score: 74.161	N	N	N	N
vg0812490623	C -> T	LOC_Os08g20800.1	intron_variant ; MODIFIER	silent_mutation	Average:50.194; most accessible tissue: Minghui63 flag leaf, score: 74.161	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812490623	NA	1.26E-12	mr1084	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
vg0812490623	NA	1.48E-06	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
vg0812490623	NA	7.91E-07	mr1194_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
vg0812490623	NA	2.80E-08	mr1746_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