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Detailed information for vg0422741082:

Variant ID: vg0422741082 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 22741082
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.62, T: 0.38, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

CAACCGTAAATCCGTTTGACTCCGTTCAACTTCCAAAATTCCTCAAATCTCGAGATCTATCTAATGGCACGCTTAGAGGTCTTTAATAGGGCTTTATTTT[T/C]
GCAGTTTGTTGAGTTGTCCTGTTTCGCGTGTAGTTTCGGAGCCCGAAAACCCGCAGTGCGAGGATTTCGAGGATCAAGCTCAAGATCTCGAGCAAGGCAA

Reverse complement sequence

TTGCCTTGCTCGAGATCTTGAGCTTGATCCTCGAAATCCTCGCACTGCGGGTTTTCGGGCTCCGAAACTACACGCGAAACAGGACAACTCAACAAACTGC[A/G]
AAAATAAAGCCCTATTAAAGACCTCTAAGCGTGCCATTAGATAGATCTCGAGATTTGAGGAATTTTGGAAGTTGAACGGAGTCAAACGGATTTACGGTTG

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	72.60%	2.40%	15.32%	9.73%	NA
All Indica	2759	65.10%	3.60%	18.56%	12.69%	NA
All Japonica	1512	97.00%	0.30%	2.65%	0.07%	NA
Aus	269	1.10%	3.00%	59.85%	36.06%	NA
Indica I	595	79.00%	1.70%	7.06%	12.27%	NA
Indica II	465	72.70%	2.60%	10.11%	14.62%	NA
Indica III	913	56.00%	5.70%	30.89%	7.45%	NA
Indica Intermediate	786	60.80%	3.30%	17.94%	17.94%	NA
Temperate Japonica	767	94.40%	0.40%	5.22%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.00%	0.20%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	1.00%	6.25%	3.12%	NA
Intermediate	90	84.40%	0.00%	5.56%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0422741082	T -> C	LOC_Os04g38220.1	upstream_gene_variant ; 3102.0bp to feature; MODIFIER	silent_mutation	Average:22.702; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0422741082	T -> C	LOC_Os04g38200.1	downstream_gene_variant ; 3230.0bp to feature; MODIFIER	silent_mutation	Average:22.702; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0422741082	T -> C	LOC_Os04g38200-LOC_Os04g38220	intergenic_region ; MODIFIER	silent_mutation	Average:22.702; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg0422741082	T -> DEL	N	N	silent_mutation	Average:22.702; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0422741082	3.51E-09	3.51E-09	mr1343	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
vg0422741082	NA	3.59E-06	mr1354	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
vg0422741082	NA	7.12E-07	mr1902	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
vg0422741082	NA	3.70E-08	mr1354_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
vg0422741082	NA	1.85E-06	mr1902_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