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Detailed information for vg0209830497:

Variant ID: vg0209830497 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9830497
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

GAATATCCCACTGTCCTCGGGTAAATAGGAGTATCATTTTATAATTTGTGTGGTTGTGTGGTCAAATATCAAAATCTTATATCACTAACGTGTGTAGAAG[T/C]
ACTAAGATTTGATATGCGAAACTAACGCTGGTAGATTTGTACTATAAAATATACTGTCGTGCAACTATATTTAAATAATATTAGAATGACTAAACATGGG

Reverse complement sequence

CCCATGTTTAGTCATTCTAATATTATTTAAATATAGTTGCACGACAGTATATTTTATAGTACAAATCTACCAGCGTTAGTTTCGCATATCAAATCTTAGT[A/G]
CTTCTACACACGTTAGTGATATAAGATTTTGATATTTGACCACACAACCACACAAATTATAAAATGATACTCCTATTTACCCGAGGACAGTGGGATATTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.10%	0.80%	0.17%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.00%	NA
All Japonica	1512	97.30%	2.20%	0.46%	0.00%	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	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	94.80%	4.40%	0.78%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0209830497	T -> C	LOC_Os02g17150.1	upstream_gene_variant ; 1385.0bp to feature; MODIFIER	N	Average:43.843; most accessible tissue: Zhenshan97 root, score: 78.63	N	N	N	N
vg0209830497	T -> C	LOC_Os02g17160.1	upstream_gene_variant ; 1084.0bp to feature; MODIFIER	N	Average:43.843; most accessible tissue: Zhenshan97 root, score: 78.63	N	N	N	N
vg0209830497	T -> C	LOC_Os02g17150-LOC_Os02g17160	intergenic_region ; MODIFIER	N	Average:43.843; most accessible tissue: Zhenshan97 root, score: 78.63	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209830497	2.90E-06	2.90E-06	mr1470	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