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Detailed information for vg0625001665:

Variant ID: vg0625001665 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 25001665
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.22, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

GCACGAACTTCAAAACATAATGTATATATAACAAGTGAGATCATATATTAATATTAATAGTATAGTAAACAACTATTATATGAATTGACTATTATATTGG[T/C]
TATAAATGAATTGAAACTAGTAGTGGGTTATACTACTCCCTCCATCCCATATTAGTTGTTGTTCCAGGTAATTTAGCATCGATTAAGGTTTGAGAAAAAA

Reverse complement sequence

TTTTTTCTCAAACCTTAATCGATGCTAAATTACCTGGAACAACAACTAATATGGGATGGAGGGAGTAGTATAACCCACTACTAGTTTCAATTCATTTATA[A/G]
CCAATATAATAGTCAATTCATATAATAGTTGTTTACTATACTATTAATATTAATATATGATCTCACTTGTTATATATACATTATGTTTTGAAGTTCGTGC

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	74.80%	25.20%	0.06%	0.00%	NA
All Indica	2759	96.00%	3.90%	0.07%	0.00%	NA
All Japonica	1512	37.60%	62.40%	0.00%	0.00%	NA
Aus	269	90.70%	9.30%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	94.80%	5.20%	0.00%	0.00%	NA
Indica III	913	98.60%	1.30%	0.11%	0.00%	NA
Indica Intermediate	786	91.00%	9.00%	0.00%	0.00%	NA
Temperate Japonica	767	43.70%	56.30%	0.00%	0.00%	NA
Tropical Japonica	504	29.60%	70.40%	0.00%	0.00%	NA
Japonica Intermediate	241	34.90%	65.10%	0.00%	0.00%	NA
VI/Aromatic	96	20.80%	79.20%	0.00%	0.00%	NA
Intermediate	90	57.80%	41.10%	1.11%	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
vg0625001665	T -> C	LOC_Os06g41710.1	upstream_gene_variant ; 3561.0bp to feature; MODIFIER	silent_mutation	Average:44.34; most accessible tissue: Zhenshan97 root, score: 70.081	N	N	N	N
vg0625001665	T -> C	LOC_Os06g41710-LOC_Os06g41720	intergenic_region ; MODIFIER	silent_mutation	Average:44.34; most accessible tissue: Zhenshan97 root, score: 70.081	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0625001665	7.03E-07	7.03E-07	mr1571_2	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
vg0625001665	NA	4.08E-07	mr1623_2	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