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Detailed information for vg0105021483:

Variant ID: vg0105021483 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5021483
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

GGATGAGGAACTACATCAACTTTGGTAGTTTGGTTGCCTCTTCCCATCTGCTTGTTCTTTAAGAGAACCTCTCTTCTCTTCCGCATGAGATATGTCAATT[G/C]
AAGAACTCATTCAGCTAAGCTGCGTCCTCCACAACTATAAAACCCAATGTGGGAGTTTCAGTAAATGAATACTCTATATCTTGTAAAAACACCAACAACA

Reverse complement sequence

TGTTGTTGGTGTTTTTACAAGATATAGAGTATTCATTTACTGAAACTCCCACATTGGGTTTTATAGTTGTGGAGGACGCAGCTTAGCTGAATGAGTTCTT[C/G]
AATTGACATATCTCATGCGGAAGAGAAGAGAGGTTCTCTTAAAGAACAAGCAGATGGGAAGAGGCAACCAAACTACCAAAGTTGATGTAGTTCCTCATCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.40%	6.20%	0.40%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	80.70%	18.10%	1.26%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	67.50%	30.10%	2.35%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	82.60%	17.00%	0.41%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0105021483	G -> C	LOC_Os01g09750.1	3_prime_UTR_variant ; 676.0bp to feature; MODIFIER	silent_mutation	Average:52.538; most accessible tissue: Callus, score: 89.297	N	N	N	N
vg0105021483	G -> C	LOC_Os01g09740.1	upstream_gene_variant ; 1333.0bp to feature; MODIFIER	silent_mutation	Average:52.538; most accessible tissue: Callus, score: 89.297	N	N	N	N
vg0105021483	G -> C	LOC_Os01g09730.1	downstream_gene_variant ; 2831.0bp to feature; MODIFIER	silent_mutation	Average:52.538; most accessible tissue: Callus, score: 89.297	N	N	N	N
vg0105021483	G -> C	LOC_Os01g09730.2	downstream_gene_variant ; 3594.0bp to feature; MODIFIER	silent_mutation	Average:52.538; most accessible tissue: Callus, score: 89.297	N	N	N	N
vg0105021483	G -> C	LOC_Os01g09750.2	downstream_gene_variant ; 568.0bp to feature; MODIFIER	silent_mutation	Average:52.538; most accessible tissue: Callus, score: 89.297	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105021483	NA	7.83E-07	mr1057	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
vg0105021483	NA	5.13E-07	mr1382	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
vg0105021483	NA	1.03E-07	mr1829	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
vg0105021483	4.22E-06	4.22E-06	mr1036_2	Jap_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
vg0105021483	2.85E-09	1.16E-12	mr1057_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
vg0105021483	NA	5.51E-07	mr1567_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
vg0105021483	NA	5.33E-10	mr1829_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
vg0105021483	NA	3.41E-06	mr1923_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