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Detailed information for vg1125812120:

Variant ID: vg1125812120 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25812120
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCTTTTTTAGAATCCTTCCCAAAAATTTCTCAAAAGATTCCCTCTGGAGCCAATATGTACCATATAGGTAGACAAGCCACCCCAGCATGTATCCCAGC[T/C]
GCACGGCCTGACCTATTGTTAATTTTTCAAAGCACTGCCCATCACAAATAGCACCACTTTGAACAACTCAACTCCCAAGAAATGGATTTAAAATGCAACC

Reverse complement sequence

GGTTGCATTTTAAATCCATTTCTTGGGAGTTGAGTTGTTCAAAGTGGTGCTATTTGTGATGGGCAGTGCTTTGAAAAATTAACAATAGGTCAGGCCGTGC[A/G]
GCTGGGATACATGCTGGGGTGGCTTGTCTACCTATATGGTACATATTGGCTCCAGAGGGAATCTTTTGAGAAATTTTTGGGAAGGATTCTAAAAAAGGAA

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	71.70%	28.10%	0.19%	0.00%	NA
All Indica	2759	58.60%	41.10%	0.25%	0.00%	NA
All Japonica	1512	90.10%	9.90%	0.00%	0.00%	NA
Aus	269	94.80%	5.20%	0.00%	0.00%	NA
Indica I	595	58.70%	41.00%	0.34%	0.00%	NA
Indica II	465	67.50%	32.00%	0.43%	0.00%	NA
Indica III	913	49.70%	50.30%	0.00%	0.00%	NA
Indica Intermediate	786	63.70%	35.90%	0.38%	0.00%	NA
Temperate Japonica	767	97.40%	2.60%	0.00%	0.00%	NA
Tropical Japonica	504	78.80%	21.20%	0.00%	0.00%	NA
Japonica Intermediate	241	90.50%	9.50%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	64.40%	34.40%	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
vg1125812120	T -> C	LOC_Os11g42850.1	upstream_gene_variant ; 1733.0bp to feature; MODIFIER	silent_mutation	Average:52.77; most accessible tissue: Callus, score: 67.906	N	N	N	N
vg1125812120	T -> C	LOC_Os11g42850.2	upstream_gene_variant ; 1733.0bp to feature; MODIFIER	silent_mutation	Average:52.77; most accessible tissue: Callus, score: 67.906	N	N	N	N
vg1125812120	T -> C	LOC_Os11g42860.1	intron_variant ; MODIFIER	silent_mutation	Average:52.77; most accessible tissue: Callus, score: 67.906	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125812120	1.26E-18	7.55E-26	mr1191	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
vg1125812120	5.52E-15	7.15E-20	mr1191	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
vg1125812120	1.25E-06	1.25E-06	mr1191	Jap_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
vg1125812120	1.49E-06	NA	mr1238	Jap_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
vg1125812120	NA	3.91E-06	mr1309	Jap_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
vg1125812120	NA	3.01E-07	mr1561	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
vg1125812120	2.54E-26	1.18E-36	mr1644	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
vg1125812120	2.84E-22	1.70E-31	mr1644	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
vg1125812120	3.17E-07	3.17E-07	mr1644	Jap_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
vg1125812120	NA	7.01E-06	mr1908	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
vg1125812120	NA	6.22E-07	mr1925	Jap_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
vg1125812120	1.76E-23	1.06E-36	mr1191_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
vg1125812120	1.26E-19	5.38E-29	mr1191_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
vg1125812120	1.81E-06	1.81E-06	mr1191_2	Jap_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
vg1125812120	NA	6.74E-06	mr1561_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
vg1125812120	NA	4.69E-06	mr1908_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