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Detailed information for vg0401199285:

Variant ID: vg0401199285 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1199285
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCAAGATTTATAACTTTTAGTTTGGTCATGTTTCTATATAACATTTTTTTGAACAGTTTGAATTTGAATTTGAAAATATGACAACTTCAAACAACATTTT[C/T]
AAATACTAAATGATTTCAATTGAAAAAGTCATTAACAACAAAGTTGAATAACTCATCAAGATCTAAAACTTTTATTTTTGTTATTTCTTCATCCGACGAA

Reverse complement sequence

TTCGTCGGATGAAGAAATAACAAAAATAAAAGTTTTAGATCTTGATGAGTTATTCAACTTTGTTGTTAATGACTTTTTCAATTGAAATCATTTAGTATTT[G/A]
AAAATGTTGTTTGAAGTTGTCATATTTTCAAATTCAAATTCAAACTGTTCAAAAAAATGTTATATAGAAACATGACCAAACTAAAAGTTATAAATCTTGA

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	88.20%	5.70%	6.16%	0.00%	NA
All Indica	2759	96.10%	1.80%	2.07%	0.00%	NA
All Japonica	1512	71.20%	13.80%	15.08%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.50%	0.80%	0.67%	0.00%	NA
Indica II	465	97.60%	1.10%	1.29%	0.00%	NA
Indica III	913	96.30%	1.80%	1.97%	0.00%	NA
Indica Intermediate	786	93.30%	3.10%	3.69%	0.00%	NA
Temperate Japonica	767	90.60%	2.50%	6.91%	0.00%	NA
Tropical Japonica	504	49.00%	26.20%	24.80%	0.00%	NA
Japonica Intermediate	241	55.60%	23.70%	20.75%	0.00%	NA
VI/Aromatic	96	94.80%	4.20%	1.04%	0.00%	NA
Intermediate	90	87.80%	6.70%	5.56%	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
vg0401199285	C -> T	LOC_Os04g02970.1	upstream_gene_variant ; 1917.0bp to feature; MODIFIER	silent_mutation	Average:17.388; most accessible tissue: Callus, score: 22.56	N	N	N	N
vg0401199285	C -> T	LOC_Os04g02960.1	downstream_gene_variant ; 2189.0bp to feature; MODIFIER	silent_mutation	Average:17.388; most accessible tissue: Callus, score: 22.56	N	N	N	N
vg0401199285	C -> T	LOC_Os04g02960-LOC_Os04g02970	intergenic_region ; MODIFIER	silent_mutation	Average:17.388; most accessible tissue: Callus, score: 22.56	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401199285	2.84E-06	NA	mr1969	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