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Detailed information for vg0322360535:

Variant ID: vg0322360535 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22360535
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTATAGTCGTGCCACTCAAATTTTATAAAATTGTAACTATGCCATCGCCATCACGTTTTTTATCTTCTTCATCATTTGCACGTGGGACCCACCCGTCA[G/T]
ATTCATCTTCTTCCTTTCACCCTCCCTTATCATATTCCTCACCATCTCTCTGTACGGCGGATGGGAGGAGCGGACGAGCAGCGAGGTGGCGGCCGTCATT

Reverse complement sequence

AATGACGGCCGCCACCTCGCTGCTCGTCCGCTCCTCCCATCCGCCGTACAGAGAGATGGTGAGGAATATGATAAGGGAGGGTGAAAGGAAGAAGATGAAT[C/A]
TGACGGGTGGGTCCCACGTGCAAATGATGAAGAAGATAAAAAACGTGATGGCGATGGCATAGTTACAATTTTATAAAATTTGAGTGGCACGACTATAAAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.80%	5.80%	1.42%	0.00%	NA
All Indica	2759	88.10%	9.50%	2.32%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.30%	3.70%	4.03%	0.00%	NA
Indica II	465	98.30%	1.30%	0.43%	0.00%	NA
Indica III	913	84.10%	15.30%	0.55%	0.00%	NA
Indica Intermediate	786	83.70%	12.10%	4.20%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	5.60%	3.33%	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
vg0322360535	G -> T	LOC_Os03g40220.1	upstream_gene_variant ; 818.0bp to feature; MODIFIER	silent_mutation	Average:44.819; most accessible tissue: Zhenshan97 young leaf, score: 61.386	N	N	N	N
vg0322360535	G -> T	LOC_Os03g40230.1	downstream_gene_variant ; 644.0bp to feature; MODIFIER	silent_mutation	Average:44.819; most accessible tissue: Zhenshan97 young leaf, score: 61.386	N	N	N	N
vg0322360535	G -> T	LOC_Os03g40220-LOC_Os03g40230	intergenic_region ; MODIFIER	silent_mutation	Average:44.819; most accessible tissue: Zhenshan97 young leaf, score: 61.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322360535	7.48E-06	9.72E-07	mr1631_2	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