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Detailed information for vg0335362475:

Variant ID: vg0335362475 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35362475
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.07, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TATAGAGCATTCATCAATATCTGCAAACAGAAAACTAAAAATGTGAACTTTAATATATCAAACTCTTGATGGCTCCTATATGCTTTTGTTTTCAATTAAA[T/C]
GCACATTAACTACAACTTCCACACTATGAAAATCATTGGATAACATATCACTCTCTTCAGATATTCCATATCTCCATGCTCCTGCCACATACAAGAAAAT

Reverse complement sequence

ATTTTCTTGTATGTGGCAGGAGCATGGAGATATGGAATATCTGAAGAGAGTGATATGTTATCCAATGATTTTCATAGTGTGGAAGTTGTAGTTAATGTGC[A/G]
TTTAATTGAAAACAAAAGCATATAGGAGCCATCAAGAGTTTGATATATTAAAGTTCACATTTTTAGTTTTCTGTTTGCAGATATTGATGAATGCTCTATA

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	65.20%	34.70%	0.13%	0.00%	NA
All Indica	2759	42.10%	57.70%	0.18%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	68.60%	31.40%	0.00%	0.00%	NA
Indica II	465	29.20%	70.30%	0.43%	0.00%	NA
Indica III	913	30.70%	69.20%	0.11%	0.00%	NA
Indica Intermediate	786	42.90%	56.90%	0.25%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	62.20%	37.80%	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
vg0335362475	T -> C	LOC_Os03g62420.1	upstream_gene_variant ; 3615.0bp to feature; MODIFIER	silent_mutation	Average:42.257; most accessible tissue: Callus, score: 83.93	N	N	N	N
vg0335362475	T -> C	LOC_Os03g62450.1	upstream_gene_variant ; 4493.0bp to feature; MODIFIER	silent_mutation	Average:42.257; most accessible tissue: Callus, score: 83.93	N	N	N	N
vg0335362475	T -> C	LOC_Os03g62440.1	downstream_gene_variant ; 3320.0bp to feature; MODIFIER	silent_mutation	Average:42.257; most accessible tissue: Callus, score: 83.93	N	N	N	N
vg0335362475	T -> C	LOC_Os03g62430.1	intron_variant ; MODIFIER	silent_mutation	Average:42.257; most accessible tissue: Callus, score: 83.93	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0335362475	4.55E-06	NA	mr1504_2	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