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Detailed information for vg0140082114:

Variant ID: vg0140082114 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 40082114
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.52, T: 0.48, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

CCTGGTCGCCGCTCAGCTAGGGTTCGAGCAAAGGAGAGAGAATGGAGGTCTGGCTAGCTGCGCTCCCCTCCATTAACCCCGTCTATTAACTCCCCAACGG[T/C]
GGACTGATCAGTGGGTCCCACAGCGCGACACGTCAGCAAAACCGGGCAAAAACTGAGTCAATACTGCCGAGGGACCTTGATGTGACCATGGCTACTACGG

Reverse complement sequence

CCGTAGTAGCCATGGTCACATCAAGGTCCCTCGGCAGTATTGACTCAGTTTTTGCCCGGTTTTGCTGACGTGTCGCGCTGTGGGACCCACTGATCAGTCC[A/G]
CCGTTGGGGAGTTAATAGACGGGGTTAATGGAGGGGAGCGCAGCTAGCCAGACCTCCATTCTCTCTCCTTTGCTCGAACCCTAGCTGAGCGGCGACCAGG

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	61.30%	38.60%	0.08%	0.00%	NA
All Indica	2759	91.80%	8.10%	0.14%	0.00%	NA
All Japonica	1512	2.10%	97.90%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.50%	3.00%	0.50%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	92.40%	7.40%	0.11%	0.00%	NA
Indica Intermediate	786	83.50%	16.50%	0.00%	0.00%	NA
Temperate Japonica	767	1.30%	98.70%	0.00%	0.00%	NA
Tropical Japonica	504	2.20%	97.80%	0.00%	0.00%	NA
Japonica Intermediate	241	4.10%	95.90%	0.00%	0.00%	NA
VI/Aromatic	96	25.00%	75.00%	0.00%	0.00%	NA
Intermediate	90	47.80%	52.20%	0.00%	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
vg0140082114	T -> C	LOC_Os01g69000.1	upstream_gene_variant ; 2280.0bp to feature; MODIFIER	silent_mutation	Average:51.12; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg0140082114	T -> C	LOC_Os01g68990.1	intron_variant ; MODIFIER	silent_mutation	Average:51.12; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0140082114	NA	2.24E-26	mr1072	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
vg0140082114	NA	3.87E-06	mr1086	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
vg0140082114	NA	4.24E-06	mr1125	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
vg0140082114	NA	4.19E-22	mr1155	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
vg0140082114	NA	3.98E-07	mr1155	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
vg0140082114	NA	6.00E-08	mr1162	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
vg0140082114	NA	6.75E-29	mr1202	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
vg0140082114	NA	3.59E-08	mr1213	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
vg0140082114	NA	7.49E-12	mr1281	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
vg0140082114	NA	2.11E-11	mr1630	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
vg0140082114	NA	2.65E-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
vg0140082114	NA	9.19E-06	mr1795	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
vg0140082114	NA	1.20E-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