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Detailed information for vg0906567849:

Variant ID: vg0906567849 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6567849
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.29, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

ACGGGCATATTTGATATTTTGTCCCGGTTGGTAACACCAACCGGGACTAAAGATCATCTTTTGTCCCGGTTCAAATGCTGTCAGGTCTTGGCAGGCCCCC[T/C]
CGGGATCTTTAGTCCCAGTTGGTAACTGCAACCGAGACTAAAGATCGTAACTTTAGTCCCGGTTGGTGATCCCGGCGATCTTTAGCTCCGGTTCATAACA

Reverse complement sequence

TGTTATGAACCGGAGCTAAAGATCGCCGGGATCACCAACCGGGACTAAAGTTACGATCTTTAGTCTCGGTTGCAGTTACCAACTGGGACTAAAGATCCCG[A/G]
GGGGGCCTGCCAAGACCTGACAGCATTTGAACCGGGACAAAAGATGATCTTTAGTCCCGGTTGGTGTTACCAACCGGGACAAAATATCAAATATGCCCGT

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	63.90%	35.90%	0.19%	0.00%	NA
All Indica	2759	77.20%	22.60%	0.18%	0.00%	NA
All Japonica	1512	51.70%	48.30%	0.00%	0.00%	NA
Aus	269	6.70%	93.30%	0.00%	0.00%	NA
Indica I	595	79.30%	20.20%	0.50%	0.00%	NA
Indica II	465	63.40%	36.60%	0.00%	0.00%	NA
Indica III	913	89.70%	10.10%	0.22%	0.00%	NA
Indica Intermediate	786	69.30%	30.70%	0.00%	0.00%	NA
Temperate Japonica	767	88.50%	11.50%	0.00%	0.00%	NA
Tropical Japonica	504	7.90%	92.10%	0.00%	0.00%	NA
Japonica Intermediate	241	25.70%	74.30%	0.00%	0.00%	NA
VI/Aromatic	96	46.90%	52.10%	1.04%	0.00%	NA
Intermediate	90	51.10%	45.60%	3.33%	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
vg0906567849	T -> C	LOC_Os09g11750.1	upstream_gene_variant ; 941.0bp to feature; MODIFIER	silent_mutation	Average:38.919; most accessible tissue: Minghui63 flag leaf, score: 62.47	N	N	N	N
vg0906567849	T -> C	LOC_Os09g11740-LOC_Os09g11750	intergenic_region ; MODIFIER	silent_mutation	Average:38.919; most accessible tissue: Minghui63 flag leaf, score: 62.47	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906567849	NA	1.07E-13	mr1570	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
vg0906567849	NA	3.94E-09	mr1593	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
vg0906567849	NA	1.50E-10	mr1769	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
vg0906567849	NA	2.34E-14	mr1593_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
vg0906567849	NA	4.68E-10	mr1769_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