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Detailed information for vg0207032362:

Variant ID: vg0207032362 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7032362
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGAACATTATAGGGGCAAGTCATTCAAACATACATAAACCTTAATTGTACTGCTAATATATCGAGCATTTGGCACAAATCAGTTGACAACCCAGCTGG[C/T]
AAATTAATTAATATATCGACTGATAACGCCGTGTAATATATTATCCTGATCAGACAGATTGTGCACTGGCATAGAACATCGACAAAACTAAAGATAATTA

Reverse complement sequence

TAATTATCTTTAGTTTTGTCGATGTTCTATGCCAGTGCACAATCTGTCTGATCAGGATAATATATTACACGGCGTTATCAGTCGATATATTAATTAATTT[G/A]
CCAGCTGGGTTGTCAACTGATTTGTGCCAAATGCTCGATATATTAGCAGTACAATTAAGGTTTATGTATGTTTGAATGACTTGCCCCTATAATGTTCAAA

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	68.40%	31.10%	0.40%	0.13%	NA
All Indica	2759	79.80%	19.50%	0.47%	0.22%	NA
All Japonica	1512	42.10%	57.70%	0.20%	0.00%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	72.60%	26.90%	0.34%	0.17%	NA
Indica II	465	89.70%	9.50%	0.43%	0.43%	NA
Indica III	913	81.40%	18.20%	0.22%	0.22%	NA
Indica Intermediate	786	77.50%	21.50%	0.89%	0.13%	NA
Temperate Japonica	767	72.90%	26.90%	0.26%	0.00%	NA
Tropical Japonica	504	6.90%	93.10%	0.00%	0.00%	NA
Japonica Intermediate	241	17.80%	81.70%	0.41%	0.00%	NA
VI/Aromatic	96	67.70%	31.20%	1.04%	0.00%	NA
Intermediate	90	73.30%	24.40%	2.22%	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
vg0207032362	C -> T	LOC_Os02g13200.1	3_prime_UTR_variant ; 277.0bp to feature; MODIFIER	silent_mutation	Average:58.66; most accessible tissue: Zhenshan97 root, score: 69.506	N	N	N	N
vg0207032362	C -> T	LOC_Os02g13190.1	upstream_gene_variant ; 4058.0bp to feature; MODIFIER	silent_mutation	Average:58.66; most accessible tissue: Zhenshan97 root, score: 69.506	N	N	N	N
vg0207032362	C -> DEL	N	N	silent_mutation	Average:58.66; most accessible tissue: Zhenshan97 root, score: 69.506	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207032362	NA	5.52E-07	mr1091	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0207032362	NA	8.28E-07	mr1229	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0207032362	NA	1.34E-09	mr1486	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0207032362	NA	5.50E-06	mr1161_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0207032362	NA	8.73E-08	mr1383_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0207032362	NA	6.87E-11	mr1530_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251