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Detailed information for vg0911132200:

Variant ID: vg0911132200 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11132200
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TAACGATCGTACTGATCATCAGGAAACCTGTATTTATGAAATCCTGAATATGAAAGGAAACATGCAATTGAAAAACAAATTGACGATGAATACTTACTTC[C/G]
TCTGGTCGTAAATATTTGACTAGTCCTAAAATTTGATGTTTGTGACAATATAAAACTTTGACCATCAACCATCAAAAAGGAAATGAGTTATGTTGAAAAA

Reverse complement sequence

TTTTTCAACATAACTCATTTCCTTTTTGATGGTTGATGGTCAAAGTTTTATATTGTCACAAACATCAAATTTTAGGACTAGTCAAATATTTACGACCAGA[G/C]
GAAGTAAGTATTCATCGTCAATTTGTTTTTCAATTGCATGTTTCCTTTCATATTCAGGATTTCATAAATACAGGTTTCCTGATGATCAGTACGATCGTTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.30%	1.40%	0.44%	3.94%	NA
All Indica	2759	97.40%	0.80%	0.22%	1.59%	NA
All Japonica	1512	99.80%	0.00%	0.07%	0.13%	NA
Aus	269	32.30%	16.00%	4.83%	46.84%	NA
Indica I	595	97.80%	0.70%	0.34%	1.18%	NA
Indica II	465	94.40%	2.40%	0.43%	2.80%	NA
Indica III	913	99.10%	0.00%	0.00%	0.88%	NA
Indica Intermediate	786	96.90%	0.80%	0.25%	2.04%	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	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	85.40%	0.00%	0.00%	14.58%	NA
Intermediate	90	98.90%	0.00%	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
vg0911132200	C -> G	LOC_Os09g18159.1	intron_variant ; MODIFIER	silent_mutation	Average:42.181; most accessible tissue: Callus, score: 68.778	N	N	N	N
vg0911132200	C -> DEL	N	N	silent_mutation	Average:42.181; most accessible tissue: Callus, score: 68.778	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911132200	NA	4.73E-20	mr1305_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
vg0911132200	NA	1.04E-12	mr1409_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
vg0911132200	1.51E-07	NA	mr1585_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