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Detailed information for vg0121499838:

Variant ID: vg0121499838 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21499838
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGATTGGGACTACCTATATATTTGTCGATAAATTTTTCCCCAAAAATTTGACAGATGTAATTATAGTACAATCGTAGTGTAATTACACTGTAACTTGCAT[G/A]
TAACTACAGTGTAACTTATACGTAAGTTTCACATAATTTTGAATCGTTTGATCTATTACAAGATTTGTTTTGGTGAGAAAGAAAACAAATCATAGCACAC

Reverse complement sequence

GTGTGCTATGATTTGTTTTCTTTCTCACCAAAACAAATCTTGTAATAGATCAAACGATTCAAAATTATGTGAAACTTACGTATAAGTTACACTGTAGTTA[C/T]
ATGCAAGTTACAGTGTAATTACACTACGATTGTACTATAATTACATCTGTCAAATTTTTGGGGAAAAATTTATCGACAAATATATAGGTAGTCCCAATCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.30%	0.70%	0.78%	53.20%	NA
All Indica	2759	18.40%	1.20%	1.30%	79.12%	NA
All Japonica	1512	97.40%	0.00%	0.00%	2.65%	NA
Aus	269	13.00%	0.00%	0.00%	86.99%	NA
Indica I	595	37.00%	1.50%	2.18%	59.33%	NA
Indica II	465	20.40%	1.30%	0.86%	77.42%	NA
Indica III	913	3.40%	1.10%	1.20%	94.30%	NA
Indica Intermediate	786	20.60%	0.90%	1.02%	77.48%	NA
Temperate Japonica	767	98.40%	0.00%	0.00%	1.56%	NA
Tropical Japonica	504	97.60%	0.00%	0.00%	2.38%	NA
Japonica Intermediate	241	93.40%	0.00%	0.00%	6.64%	NA
VI/Aromatic	96	69.80%	0.00%	0.00%	30.21%	NA
Intermediate	90	67.80%	0.00%	1.11%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0121499838	G -> A	LOC_Os01g38320.1	downstream_gene_variant ; 4430.0bp to feature; MODIFIER	silent_mutation	Average:8.899; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0121499838	G -> A	LOC_Os01g38320-LOC_Os01g38330	intergenic_region ; MODIFIER	silent_mutation	Average:8.899; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0121499838	G -> DEL	N	N	silent_mutation	Average:8.899; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121499838	4.05E-06	1.09E-06	mr1182	Ind_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