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Detailed information for vg1000093464:

Variant ID: vg1000093464 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 93464
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

GGTAGCGTTTGACGAAACTTCTAGAAATTATAAAAAAGAAGCCCAACATGACAATAAACTCTAAAAACTATAAGTTTTTATATCCAAATTTTAAAGGTTT[C/T]
AAGGAGAATGAATAGAAACAGTGGTTGATCGAGCAAGTAAATAAATAATAATATAACAGAAGTAAGGGCTAGTAACTGGTGTGACTTTTAAAAACTATAA

Reverse complement sequence

TTATAGTTTTTAAAAGTCACACCAGTTACTAGCCCTTACTTCTGTTATATTATTATTTATTTACTTGCTCGATCAACCACTGTTTCTATTCATTCTCCTT[G/A]
AAACCTTTAAAATTTGGATATAAAAACTTATAGTTTTTAGAGTTTATTGTCATGTTGGGCTTCTTTTTTATAATTTCTAGAAGTTTCGTCAAACGCTACC

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	58.60%	41.00%	0.38%	0.00%	NA
All Indica	2759	33.90%	65.50%	0.62%	0.00%	NA
All Japonica	1512	98.40%	1.60%	0.00%	0.00%	NA
Aus	269	68.00%	32.00%	0.00%	0.00%	NA
Indica I	595	37.00%	62.00%	1.01%	0.00%	NA
Indica II	465	41.70%	57.80%	0.43%	0.00%	NA
Indica III	913	31.30%	68.30%	0.33%	0.00%	NA
Indica Intermediate	786	29.90%	69.30%	0.76%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	97.20%	2.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	23.30%	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
vg1000093464	C -> T	LOC_Os10g01100.1	upstream_gene_variant ; 1334.0bp to feature; MODIFIER	silent_mutation	Average:48.796; most accessible tissue: Callus, score: 76.223	N	N	N	N
vg1000093464	C -> T	LOC_Os10g01090-LOC_Os10g01100	intergenic_region ; MODIFIER	silent_mutation	Average:48.796; most accessible tissue: Callus, score: 76.223	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000093464	NA	9.92E-07	mr1168	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
vg1000093464	NA	7.58E-07	mr1383	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
vg1000093464	NA	8.55E-13	mr1449	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
vg1000093464	2.36E-06	3.10E-08	mr1158_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
vg1000093464	1.95E-06	NA	mr1168_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
vg1000093464	5.49E-07	7.26E-10	mr1168_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
vg1000093464	9.92E-06	NA	mr1383_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
vg1000093464	2.24E-06	NA	mr1383_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
vg1000093464	NA	3.46E-06	mr1486_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
vg1000093464	NA	1.98E-07	mr1855_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