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Detailed information for vg0309106481:

Variant ID: vg0309106481 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 9106481
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, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

CTGTATATGTATAACGGCTAGGTGACGTCATCTAGCCGTTACTCACAAATTTGAACTGGAAACAAGACAGGAAGTTCCGGACCTGGAAGACCGGAACTTC[C/T]
GGACTACACTTAGGAAAATCTTTTTCACAAGACCGGAACTTCTAGACCTAGAAGACAGGAAGTTCCGGACTTGCATTTTTGGACAGATGGAGTATTTGCA

Reverse complement sequence

TGCAAATACTCCATCTGTCCAAAAATGCAAGTCCGGAACTTCCTGTCTTCTAGGTCTAGAAGTTCCGGTCTTGTGAAAAAGATTTTCCTAAGTGTAGTCC[G/A]
GAAGTTCCGGTCTTCCAGGTCCGGAACTTCCTGTCTTGTTTCCAGTTCAAATTTGTGAGTAACGGCTAGATGACGTCACCTAGCCGTTATACATATACAG

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	94.60%	0.10%	4.80%	0.49%	NA
All Indica	2759	90.80%	0.20%	8.19%	0.83%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	93.10%	0.00%	6.05%	0.84%	NA
Indica II	465	92.50%	0.20%	6.24%	1.08%	NA
Indica III	913	90.40%	0.30%	8.87%	0.44%	NA
Indica Intermediate	786	88.50%	0.10%	10.18%	1.15%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	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
vg0309106481	C -> T	LOC_Os03g16530.1	downstream_gene_variant ; 1074.0bp to feature; MODIFIER	silent_mutation	Average:28.744; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N
vg0309106481	C -> T	LOC_Os03g16500-LOC_Os03g16530	intergenic_region ; MODIFIER	silent_mutation	Average:28.744; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N
vg0309106481	C -> DEL	N	N	silent_mutation	Average:28.744; most accessible tissue: Zhenshan97 root, score: 49.075	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0309106481	NA	9.45E-07	mr1004	Ind_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
vg0309106481	NA	2.27E-06	mr1005	Ind_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
vg0309106481	NA	8.45E-07	mr1011	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
vg0309106481	NA	1.30E-06	mr1011	Ind_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
vg0309106481	7.47E-07	7.44E-07	mr1012	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
vg0309106481	2.40E-06	1.52E-07	mr1012	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
vg0309106481	NA	6.95E-06	mr1163	Ind_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