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Detailed information for vg1119404611:

Variant ID: vg1119404611 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19404611
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.22, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

ATTATTTTGGTGGTTAGTGATAATCTGATTATTGAGGACTGATGTTTGTAGTTGAGAATGTATGAAAGAATATTAGTCCGGCATGAGTCGATGTTCGATG[C/T]
AATATCGTTATATATGGGAGTTTTGATGAAAATGGGCAAAGAACCTATATTGATAAACTGTAGAGAGTGAGAGGAGTCGTTATACCGGTTTTGTAGTTGA

Reverse complement sequence

TCAACTACAAAACCGGTATAACGACTCCTCTCACTCTCTACAGTTTATCAATATAGGTTCTTTGCCCATTTTCATCAAAACTCCCATATATAACGATATT[G/A]
CATCGAACATCGACTCATGCCGGACTAATATTCTTTCATACATTCTCAACTACAAACATCAGTCCTCAATAATCAGATTATCACTAACCACCAAAATAAT

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	62.40%	37.30%	0.38%	0.00%	NA
All Indica	2759	93.10%	6.40%	0.54%	0.00%	NA
All Japonica	1512	7.20%	92.80%	0.00%	0.00%	NA
Aus	269	77.70%	21.90%	0.37%	0.00%	NA
Indica I	595	96.10%	3.50%	0.34%	0.00%	NA
Indica II	465	90.10%	8.80%	1.08%	0.00%	NA
Indica III	913	95.80%	3.90%	0.22%	0.00%	NA
Indica Intermediate	786	89.30%	9.90%	0.76%	0.00%	NA
Temperate Japonica	767	3.70%	96.30%	0.00%	0.00%	NA
Tropical Japonica	504	10.70%	89.30%	0.00%	0.00%	NA
Japonica Intermediate	241	11.20%	88.80%	0.00%	0.00%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	58.90%	38.90%	2.22%	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
vg1119404611	C -> T	LOC_Os11g32850.1	upstream_gene_variant ; 845.0bp to feature; MODIFIER	silent_mutation	Average:39.775; most accessible tissue: Zhenshan97 young leaf, score: 71.923	N	N	N	N
vg1119404611	C -> T	LOC_Os11g32840.1	downstream_gene_variant ; 891.0bp to feature; MODIFIER	silent_mutation	Average:39.775; most accessible tissue: Zhenshan97 young leaf, score: 71.923	N	N	N	N
vg1119404611	C -> T	LOC_Os11g32840-LOC_Os11g32850	intergenic_region ; MODIFIER	silent_mutation	Average:39.775; most accessible tissue: Zhenshan97 young leaf, score: 71.923	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119404611	NA	6.05E-06	mr1508	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
vg1119404611	NA	2.95E-21	mr1698	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
vg1119404611	NA	1.16E-08	mr1986	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
vg1119404611	NA	4.50E-08	mr1354_2	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
vg1119404611	NA	8.66E-06	mr1402_2	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
vg1119404611	NA	6.93E-08	mr1408_2	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
vg1119404611	NA	1.02E-07	mr1783_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