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Detailed information for vg0724557637:

Variant ID: vg0724557637 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24557637
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

CTAGGCAGCTCTTTGGGCTTGCCGGCACGATCACACCATTATAATACCATTAATTTTCAGTGATTAACATGTATAATTGTTCACACTATATGTTTGTAGC[A/C]
TATATAAATTTAACCTTGTATGTTTCTGATGTGATTTAACACATACTACCTCCGTTTTTTAATAGATGACGCCGTTAACCTTTTCTCACATGTTTGATCA

Reverse complement sequence

TGATCAAACATGTGAGAAAAGGTTAACGGCGTCATCTATTAAAAAACGGAGGTAGTATGTGTTAAATCACATCAGAAACATACAAGGTTAAATTTATATA[T/G]
GCTACAAACATATAGTGTGAACAATTATACATGTTAATCACTGAAAATTAATGGTATTATAATGGTGTGATCGTGCCGGCAAGCCCAAAGAGCTGCCTAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.50%	5.80%	1.69%	0.00%	NA
All Indica	2759	99.20%	0.40%	0.33%	0.00%	NA
All Japonica	1512	78.80%	16.70%	4.56%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.20%	0.34%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	98.60%	0.60%	0.76%	0.00%	NA
Temperate Japonica	767	61.10%	30.50%	8.34%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	91.30%	7.10%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	10.00%	2.22%	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
vg0724557637	A -> C	LOC_Os07g41050.1	downstream_gene_variant ; 912.0bp to feature; MODIFIER	silent_mutation	Average:66.15; most accessible tissue: Zhenshan97 flower, score: 88.021	N	N	N	N
vg0724557637	A -> C	LOC_Os07g41060.1	downstream_gene_variant ; 1933.0bp to feature; MODIFIER	silent_mutation	Average:66.15; most accessible tissue: Zhenshan97 flower, score: 88.021	N	N	N	N
vg0724557637	A -> C	LOC_Os07g41050-LOC_Os07g41060	intergenic_region ; MODIFIER	silent_mutation	Average:66.15; most accessible tissue: Zhenshan97 flower, score: 88.021	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724557637	NA	8.95E-07	mr1002	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
vg0724557637	3.29E-08	NA	mr1354	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
vg0724557637	2.34E-07	NA	mr1354_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