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Detailed information for vg0334893672:

Variant ID: vg0334893672 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34893672
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

GATGCAGCACTAAGTATGAAAAGAAACATTATATCTAGACAATCAAGCCGTTGACTGAGTTTTCAGGGTGGTAGATGTCTAAGCTAATCTAATCTAGAAA[C/T]
ACGATTTAGCTAATACCGGCAAAAACCCTAAAACGAGAAGCAGCCGATAGAGCTAAATTGATATGCTAAGACTAGATTAACAGAGACATATGATAAATAG

Reverse complement sequence

CTATTTATCATATGTCTCTGTTAATCTAGTCTTAGCATATCAATTTAGCTCTATCGGCTGCTTCTCGTTTTAGGGTTTTTGCCGGTATTAGCTAAATCGT[G/A]
TTTCTAGATTAGATTAGCTTAGACATCTACCACCCTGAAAACTCAGTCAACGGCTTGATTGTCTAGATATAATGTTTCTTTTCATACTTAGTGCTGCATC

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	67.80%	16.00%	1.78%	14.47%	NA
All Indica	2759	48.20%	24.80%	2.97%	23.96%	NA
All Japonica	1512	99.50%	0.20%	0.00%	0.33%	NA
Aus	269	79.20%	20.10%	0.37%	0.37%	NA
Indica I	595	71.60%	15.50%	1.51%	11.43%	NA
Indica II	465	36.80%	17.00%	1.72%	44.52%	NA
Indica III	913	40.00%	32.10%	5.26%	22.67%	NA
Indica Intermediate	786	46.90%	28.10%	2.16%	22.77%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	98.80%	0.60%	0.00%	0.60%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	94.80%	1.00%	0.00%	4.17%	NA
Intermediate	90	70.00%	14.40%	1.11%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0334893672	C -> T	LOC_Os03g61510.1	upstream_gene_variant ; 1623.0bp to feature; MODIFIER	silent_mutation	Average:16.81; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0334893672	C -> T	LOC_Os03g61530.1	downstream_gene_variant ; 1672.0bp to feature; MODIFIER	silent_mutation	Average:16.81; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0334893672	C -> T	LOC_Os03g61540.1	downstream_gene_variant ; 2660.0bp to feature; MODIFIER	silent_mutation	Average:16.81; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0334893672	C -> T	LOC_Os03g61540.2	downstream_gene_variant ; 2660.0bp to feature; MODIFIER	silent_mutation	Average:16.81; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0334893672	C -> T	LOC_Os03g61510-LOC_Os03g61530	intergenic_region ; MODIFIER	silent_mutation	Average:16.81; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0334893672	C -> DEL	N	N	silent_mutation	Average:16.81; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334893672	3.56E-06	3.33E-06	mr1863_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