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Detailed information for vg0123991825:

Variant ID: vg0123991825 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 23991825
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCTATTGTTAAGTAACTACTCCCTCCGTCTCCATAATATAAGGGATTTTGAGTTTTTGTTTGTATTGTTTGACCACTCGTCTTATTTAAAAAATTTGTG[C/T]
AAATATAAAAAACGATAAGTTGTGCTTAAAAGTACTTTGGATAATAAAGTAAGTCAAAAAAAATAAATAATAATTCCAAAATTTTTTGAATAAGACGAGT

Reverse complement sequence

ACTCGTCTTATTCAAAAAATTTTGGAATTATTATTTATTTTTTTTGACTTACTTTATTATCCAAAGTACTTTTAAGCACAACTTATCGTTTTTTATATTT[G/A]
CACAAATTTTTTAAATAAGACGAGTGGTCAAACAATACAAACAAAAACTCAAAATCCCTTATATTATGGAGACGGAGGGAGTAGTTACTTAACAATAGAC

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	93.10%	5.60%	1.29%	0.00%	NA
All Indica	2759	99.70%	0.10%	0.18%	0.00%	NA
All Japonica	1512	83.00%	13.40%	3.64%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	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	99.10%	0.50%	0.38%	0.00%	NA
Temperate Japonica	767	81.10%	12.50%	6.39%	0.00%	NA
Tropical Japonica	504	80.80%	19.00%	0.20%	0.00%	NA
Japonica Intermediate	241	93.80%	4.10%	2.07%	0.00%	NA
VI/Aromatic	96	51.00%	49.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	1.11%	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
vg0123991825	C -> T	LOC_Os01g42294-LOC_Os01g42310	intergenic_region ; MODIFIER	silent_mutation	Average:66.313; most accessible tissue: Callus, score: 95.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0123991825	1.50E-06	NA	mr1923_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