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Detailed information for vg0324423821:

Variant ID: vg0324423821 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 24423821
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACGAATACACAACACTAATTTAAATCTACATTTGTAAAAATGAAAGCAACCCAATTTAGTTGTTTCATTTTACACCATTAGATTATATTTAATATTTAA[A/T]
AATAATGTATTTCTCCTATATACGGATACATGAGAAATATGTAGCTGTTGACCAGAAAAAGTACTCCATATGTACATATGATCGAAAAGAATAATATTGC

Reverse complement sequence

GCAATATTATTCTTTTCGATCATATGTACATATGGAGTACTTTTTCTGGTCAACAGCTACATATTTCTCATGTATCCGTATATAGGAGAAATACATTATT[T/A]
TTAAATATTAAATATAATCTAATGGTGTAAAATGAAACAACTAAATTGGGTTGCTTTCATTTTTACAAATGTAGATTTAAATTAGTGTTGTGTATTCGTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.20%	8.40%	0.44%	0.00%	NA
All Indica	2759	99.00%	0.70%	0.33%	0.00%	NA
All Japonica	1512	75.30%	24.10%	0.60%	0.00%	NA
Aus	269	95.50%	3.70%	0.74%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.90%	0.00%	1.08%	0.00%	NA
Indica III	913	99.20%	0.30%	0.44%	0.00%	NA
Indica Intermediate	786	98.20%	1.80%	0.00%	0.00%	NA
Temperate Japonica	767	94.50%	4.80%	0.65%	0.00%	NA
Tropical Japonica	504	44.40%	54.80%	0.79%	0.00%	NA
Japonica Intermediate	241	78.40%	21.60%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	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
vg0324423821	A -> T	LOC_Os03g43670.1	downstream_gene_variant ; 3748.0bp to feature; MODIFIER	silent_mutation	Average:42.569; most accessible tissue: Callus, score: 60.397	N	N	N	N
vg0324423821	A -> T	LOC_Os03g43684.1	downstream_gene_variant ; 2902.0bp to feature; MODIFIER	silent_mutation	Average:42.569; most accessible tissue: Callus, score: 60.397	N	N	N	N
vg0324423821	A -> T	LOC_Os03g43670-LOC_Os03g43684	intergenic_region ; MODIFIER	silent_mutation	Average:42.569; most accessible tissue: Callus, score: 60.397	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324423821	3.49E-06	3.49E-06	mr1261	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