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Detailed information for vg0712400828:

Variant ID: vg0712400828 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 12400828
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, G: 0.31, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:

CTTACCACAAGCCAGCATGGGCAACGGCTAGGCTTGTAGTGTTGCTTTCCTTTAGCCGACGTACCCAGGCGAGGGTGGGCGTGATGGAGTTGGGTCGGTC[G/C]
GGGTGTCCGGTTGATCGGCTTCCGGATTCACCGCGGCACGAAAGGGGGGCTGCCCGTTGCCTGCTGGGGACGGGGGCGAACCCTAAGGTGTGATGCGATC

Reverse complement sequence

GATCGCATCACACCTTAGGGTTCGCCCCCGTCCCCAGCAGGCAACGGGCAGCCCCCCTTTCGTGCCGCGGTGAATCCGGAAGCCGATCAACCGGACACCC[C/G]
GACCGACCCAACTCCATCACGCCCACCCTCGCCTGGGTACGTCGGCTAAAGGAAAGCAACACTACAAGCCTAGCCGTTGCCCATGCTGGCTTGTGGTAAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.40%	26.50%	0.21%	8.89%	NA
All Indica	2759	96.40%	1.70%	0.18%	1.67%	NA
All Japonica	1512	6.40%	74.40%	0.13%	19.05%	NA
Aus	269	79.60%	15.60%	0.00%	4.83%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	98.50%	1.40%	0.00%	0.11%	NA
Indica Intermediate	786	91.70%	1.90%	0.64%	5.73%	NA
Temperate Japonica	767	2.10%	65.60%	0.13%	32.20%	NA
Tropical Japonica	504	13.70%	85.70%	0.00%	0.60%	NA
Japonica Intermediate	241	5.00%	78.80%	0.41%	15.77%	NA
VI/Aromatic	96	25.00%	0.00%	3.12%	71.88%	NA
Intermediate	90	55.60%	40.00%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0712400828	G -> DEL	N	N	silent_mutation	Average:66.903; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N
vg0712400828	G -> C	LOC_Os07g22210.1	upstream_gene_variant ; 2978.0bp to feature; MODIFIER	silent_mutation	Average:66.903; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N
vg0712400828	G -> C	LOC_Os07g22210-LOC_Os07g22220	intergenic_region ; MODIFIER	silent_mutation	Average:66.903; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0712400828	NA	1.46E-14	mr1592	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
vg0712400828	NA	1.23E-26	mr1888	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
vg0712400828	NA	9.07E-06	mr1888	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
vg0712400828	NA	3.06E-09	mr1222_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