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Detailed information for vg0129211280:

Variant ID: vg0129211280 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 29211280
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTCCTATCCAGGGATATCCCTTTAACCAAATATAAACTAAGATGCTCATATGATTAATGTATACACTAGAAAAAGCGTGCGGCTTTGCCACGTGTGGTA[C/T]
AGTGAGCCTGGCTCATTAGGCCTAGTGAATAGGTAACAAATTAATACACATATATAGAAGAGCCAGATTAATAGTAGAGATAACTAAACTTATATTAGAG

Reverse complement sequence

CTCTAATATAAGTTTAGTTATCTCTACTATTAATCTGGCTCTTCTATATATGTGTATTAATTTGTTACCTATTCACTAGGCCTAATGAGCCAGGCTCACT[G/A]
TACCACACGTGGCAAAGCCGCACGCTTTTTCTAGTGTATACATTAATCATATGAGCATCTTAGTTTATATTTGGTTAAAGGGATATCCCTGGATAGGAGA

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	92.70%	7.10%	0.21%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	79.00%	20.40%	0.53%	0.00%	NA
Aus	269	96.70%	2.60%	0.74%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	90.70%	8.90%	0.39%	0.00%	NA
Tropical Japonica	504	73.00%	26.80%	0.20%	0.00%	NA
Japonica Intermediate	241	54.40%	44.00%	1.66%	0.00%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0129211280	C -> T	LOC_Os01g50849.3	upstream_gene_variant ; 1673.0bp to feature; MODIFIER	silent_mutation	Average:61.011; most accessible tissue: Minghui63 panicle, score: 84.005	N	N	N	N
vg0129211280	C -> T	LOC_Os01g50849.1	upstream_gene_variant ; 1673.0bp to feature; MODIFIER	silent_mutation	Average:61.011; most accessible tissue: Minghui63 panicle, score: 84.005	N	N	N	N
vg0129211280	C -> T	LOC_Os01g50849.2	upstream_gene_variant ; 1673.0bp to feature; MODIFIER	silent_mutation	Average:61.011; most accessible tissue: Minghui63 panicle, score: 84.005	N	N	N	N
vg0129211280	C -> T	LOC_Os01g50849-LOC_Os01g50860	intergenic_region ; MODIFIER	silent_mutation	Average:61.011; most accessible tissue: Minghui63 panicle, score: 84.005	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0129211280	4.05E-06	NA	mr1771	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
vg0129211280	NA	3.13E-06	mr1695_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