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Detailed information for vg1124840128:

Variant ID: vg1124840128 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24840128
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

CGTGCCTTGCACGTGCACACTCACTAGTATTTTAAAATGGATGAGTAGATTTATAGATTTACTCCCTCCATTTCAAAATATAAGACCCGGCCACTATTAA[T/C]
GCAAAGACAAAAAAAAATATTATCACCTTTTTGTTAGGATCACCCAAATAAATAAAATGCATGCACCCAATGGGAATAGAGTTATTGAGAATGGAGGATT

Reverse complement sequence

AATCCTCCATTCTCAATAACTCTATTCCCATTGGGTGCATGCATTTTATTTATTTGGGTGATCCTAACAAAAAGGTGATAATATTTTTTTTTGTCTTTGC[A/G]
TTAATAGTGGCCGGGTCTTATATTTTGAAATGGAGGGAGTAAATCTATAAATCTACTCATCCATTTTAAAATACTAGTGAGTGTGCACGTGCAAGGCACG

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	88.50%	10.80%	0.66%	0.00%	NA
All Indica	2759	92.30%	7.60%	0.11%	0.00%	NA
All Japonica	1512	79.10%	19.10%	1.79%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	95.00%	4.90%	0.17%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	90.80%	9.20%	0.00%	0.00%	NA
Indica Intermediate	786	88.50%	11.20%	0.25%	0.00%	NA
Temperate Japonica	767	64.10%	32.30%	3.52%	0.00%	NA
Tropical Japonica	504	96.80%	3.20%	0.00%	0.00%	NA
Japonica Intermediate	241	89.60%	10.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	11.10%	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
vg1124840128	T -> C	LOC_Os11g41380.1	downstream_gene_variant ; 3336.0bp to feature; MODIFIER	silent_mutation	Average:27.667; most accessible tissue: Zhenshan97 young leaf, score: 55.899	N	N	N	N
vg1124840128	T -> C	LOC_Os11g41400.1	downstream_gene_variant ; 3910.0bp to feature; MODIFIER	silent_mutation	Average:27.667; most accessible tissue: Zhenshan97 young leaf, score: 55.899	N	N	N	N
vg1124840128	T -> C	LOC_Os11g41390.1	intron_variant ; MODIFIER	silent_mutation	Average:27.667; most accessible tissue: Zhenshan97 young leaf, score: 55.899	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124840128	8.29E-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
vg1124840128	1.97E-07	3.16E-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
vg1124840128	2.73E-06	NA	mr1841	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
vg1124840128	6.44E-06	NA	mr1841	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
vg1124840128	3.20E-06	NA	mr1900	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
vg1124840128	7.76E-06	NA	mr1900	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
vg1124840128	5.01E-06	NA	mr1238_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
vg1124840128	3.40E-07	NA	mr1238_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
vg1124840128	NA	3.97E-06	mr1533_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
vg1124840128	1.69E-08	NA	mr1609_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
vg1124840128	3.31E-08	3.31E-08	mr1609_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
vg1124840128	6.06E-07	NA	mr1841_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
vg1124840128	9.98E-08	NA	mr1841_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
vg1124840128	6.55E-07	NA	mr1900_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
vg1124840128	1.58E-07	NA	mr1900_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