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Detailed information for vg0320823032:

Variant ID: vg0320823032 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20823032
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

ATCGAACCTGGAAGACCAGGCAAAGCTTTCGCCCAAGACTCCCTCAAGAGTGCGGAACCTCTAAGAAGCTAGAGCAAAAGTGTTGAGTGTTATCATTGCC[C/T]
AGCTTATCAGCTGAACCCGATGCAGCATCTCCGACTCCACCTTAGCACAAAAACTCTAAACCCGCAGAGGGTAAGCACACCGCTCCACACTCGGCATAAC

Reverse complement sequence

GTTATGCCGAGTGTGGAGCGGTGTGCTTACCCTCTGCGGGTTTAGAGTTTTTGTGCTAAGGTGGAGTCGGAGATGCTGCATCGGGTTCAGCTGATAAGCT[G/A]
GGCAATGATAACACTCAACACTTTTGCTCTAGCTTCTTAGAGGTTCCGCACTCTTGAGGGAGTCTTGGGCGAAAGCTTTGCCTGGTCTTCCAGGTTCGAT

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	90.60%	5.50%	0.55%	3.26%	NA
All Indica	2759	99.60%	0.30%	0.07%	0.04%	NA
All Japonica	1512	71.70%	16.70%	1.59%	9.99%	NA
Aus	269	100.00%	0.00%	0.00%	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	99.70%	0.20%	0.00%	0.11%	NA
Indica Intermediate	786	99.10%	0.60%	0.25%	0.00%	NA
Temperate Japonica	767	95.80%	3.50%	0.65%	0.00%	NA
Tropical Japonica	504	36.90%	33.70%	2.58%	26.79%	NA
Japonica Intermediate	241	67.60%	23.20%	2.49%	6.64%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0320823032	C -> T	LOC_Os03g37554.1	downstream_gene_variant ; 3536.0bp to feature; MODIFIER	silent_mutation	Average:72.304; most accessible tissue: Zhenshan97 young leaf, score: 86.698	N	N	N	N
vg0320823032	C -> T	LOC_Os03g37540.1	intron_variant ; MODIFIER	silent_mutation	Average:72.304; most accessible tissue: Zhenshan97 young leaf, score: 86.698	N	N	N	N
vg0320823032	C -> DEL	N	N	silent_mutation	Average:72.304; most accessible tissue: Zhenshan97 young leaf, score: 86.698	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320823032	3.76E-06	2.71E-07	mr1836_2	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