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Detailed information for vg1225940329:

Variant ID: vg1225940329 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 25940329
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, T: 0.31, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

TTACACTTCTGTAATAACTGTTGCTGACTTGCTGTACCTGTACATCATTAACCTGTCTAAAATTTTTTCAAATCTTTACACAAGCAGAACAATTGATGCT[C/T]
CGTGGCCGTAAAATTGTCTCTCTTGTCTGATTCCTGCAATCTTTGGACATTCAATCCAGATCTGAAATTCTTGCTGTTTCTACACAAACAAGGAGTATAC

Reverse complement sequence

GTATACTCCTTGTTTGTGTAGAAACAGCAAGAATTTCAGATCTGGATTGAATGTCCAAAGATTGCAGGAATCAGACAAGAGAGACAATTTTACGGCCACG[G/A]
AGCATCAATTGTTCTGCTTGTGTAAAGATTTGAAAAAATTTTAGACAGGTTAATGATGTACAGGTACAGCAAGTCAGCAACAGTTATTACAGAAGTGTAA

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	62.60%	37.30%	0.08%	0.00%	NA
All Indica	2759	93.80%	6.10%	0.07%	0.00%	NA
All Japonica	1512	1.10%	98.80%	0.07%	0.00%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	87.60%	12.40%	0.00%	0.00%	NA
Indica II	465	94.60%	5.20%	0.22%	0.00%	NA
Indica III	913	97.80%	2.20%	0.00%	0.00%	NA
Indica Intermediate	786	93.40%	6.50%	0.13%	0.00%	NA
Temperate Japonica	767	0.00%	99.90%	0.13%	0.00%	NA
Tropical Japonica	504	2.40%	97.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	57.30%	42.70%	0.00%	0.00%	NA
Intermediate	90	45.60%	53.30%	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
vg1225940329	C -> T	LOC_Os12g41870.1	downstream_gene_variant ; 4190.0bp to feature; MODIFIER	silent_mutation	Average:44.892; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1225940329	C -> T	LOC_Os12g41860-LOC_Os12g41870	intergenic_region ; MODIFIER	silent_mutation	Average:44.892; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1225940329	NA	2.31E-40	mr1105	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
vg1225940329	NA	4.06E-11	mr1232	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
vg1225940329	NA	9.83E-19	mr1529	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
vg1225940329	NA	1.51E-18	mr1557	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
vg1225940329	NA	1.40E-12	mr1579	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
vg1225940329	NA	4.03E-09	mr1722	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
vg1225940329	NA	1.77E-30	mr1723	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
vg1225940329	NA	1.62E-06	mr1815	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
vg1225940329	NA	4.08E-32	mr1105_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
vg1225940329	NA	3.59E-18	mr1146_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
vg1225940329	NA	9.11E-13	mr1191_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
vg1225940329	NA	3.03E-10	mr1232_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
vg1225940329	NA	5.12E-16	mr1557_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