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Detailed information for vg0303148156:

Variant ID: vg0303148156 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 3148156
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

GCGGGAGCCGGCCCACGGAGAGGACTACCCAAGCCTCGATCACTCGGGGTAGTTCTTCCTTCACTCCAAAGGTGGTGAACTCCAAACCACTCACAAACGG[T/C]
GCCGGGCCTCCTCCACAATCTCCTCGGAGAGGTCACCGGGCAACACCTACACAAGCCGTTTAAGAGGCGGCAACCTCCAAGAGTAACAAGTCTAGGATGC

Reverse complement sequence

GCATCCTAGACTTGTTACTCTTGGAGGTTGCCGCCTCTTAAACGGCTTGTGTAGGTGTTGCCCGGTGACCTCTCCGAGGAGATTGTGGAGGAGGCCCGGC[A/G]
CCGTTTGTGAGTGGTTTGGAGTTCACCACCTTTGGAGTGAAGGAAGAACTACCCCGAGTGATCGAGGCTTGGGTAGTCCTCTCCGTGGGCCGGCTCCCGC

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	36.40%	0.70%	8.46%	54.44%	NA
All Indica	2759	4.70%	1.10%	9.28%	84.96%	NA
All Japonica	1512	97.80%	0.00%	0.07%	2.12%	NA
Aus	269	3.30%	0.40%	41.64%	54.65%	NA
Indica I	595	2.70%	0.80%	5.55%	90.92%	NA
Indica II	465	7.50%	0.60%	9.89%	81.94%	NA
Indica III	913	2.60%	1.30%	11.61%	84.45%	NA
Indica Intermediate	786	7.00%	1.10%	9.03%	82.82%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	94.80%	0.00%	0.00%	5.16%	NA
Japonica Intermediate	241	98.80%	0.00%	0.41%	0.83%	NA
VI/Aromatic	96	58.30%	1.00%	26.04%	14.58%	NA
Intermediate	90	52.20%	1.10%	6.67%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0303148156	T -> C	LOC_Os03g06270.1	upstream_gene_variant ; 2166.0bp to feature; MODIFIER	silent_mutation	Average:14.73; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N
vg0303148156	T -> C	LOC_Os03g06280.1	upstream_gene_variant ; 424.0bp to feature; MODIFIER	silent_mutation	Average:14.73; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N
vg0303148156	T -> C	LOC_Os03g06290.1	downstream_gene_variant ; 3357.0bp to feature; MODIFIER	silent_mutation	Average:14.73; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N
vg0303148156	T -> C	LOC_Os03g06270-LOC_Os03g06280	intergenic_region ; MODIFIER	silent_mutation	Average:14.73; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N
vg0303148156	T -> DEL	N	N	silent_mutation	Average:14.73; most accessible tissue: Zhenshan97 root, score: 20.427	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0303148156	NA	3.50E-13	mr1035_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
vg0303148156	NA	3.95E-12	mr1216_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
vg0303148156	1.77E-07	3.02E-57	mr1526_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
vg0303148156	NA	1.44E-29	mr1631_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