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Detailed information for vg0723951270:

Variant ID: vg0723951270 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 23951270
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.16, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TCCATCAAACGATGCCACTATGCCCCTCTACAGCCCGTCCATCGCCTACTCTTTATTGTCATTGTGATTCTAAAAATCAAACATAACTATCGTTGGAATT[T/C]
ATTTTTTATTTTCTAGAAGTCCCGTCAATCGTCGGCGGCTCTACAACTATACTCTTATACACCCCGCCCGCTGCTTCTCCTTTTTATTGTCATTGAGATT

Reverse complement sequence

AATCTCAATGACAATAAAAAGGAGAAGCAGCGGGCGGGGTGTATAAGAGTATAGTTGTAGAGCCGCCGACGATTGACGGGACTTCTAGAAAATAAAAAAT[A/G]
AATTCCAACGATAGTTATGTTTGATTTTTAGAATCACAATGACAATAAAGAGTAGGCGATGGACGGGCTGTAGAGGGGCATAGTGGCATCGTTTGATGGA

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	50.10%	34.60%	15.38%	0.00%	NA
All Indica	2759	18.70%	56.30%	25.08%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	66.90%	21.60%	11.52%	0.00%	NA
Indica I	595	14.60%	60.70%	24.71%	0.00%	NA
Indica II	465	21.30%	47.50%	31.18%	0.00%	NA
Indica III	913	16.10%	61.30%	22.56%	0.00%	NA
Indica Intermediate	786	23.20%	52.20%	24.68%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	73.30%	22.20%	4.44%	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
vg0723951270	T -> C	LOC_Os07g39930.1	upstream_gene_variant ; 2135.0bp to feature; MODIFIER	silent_mutation	Average:27.927; most accessible tissue: Zhenshan97 flag leaf, score: 41.874	N	N	N	N
vg0723951270	T -> C	LOC_Os07g39920.1	downstream_gene_variant ; 806.0bp to feature; MODIFIER	silent_mutation	Average:27.927; most accessible tissue: Zhenshan97 flag leaf, score: 41.874	N	N	N	N
vg0723951270	T -> C	LOC_Os07g39920-LOC_Os07g39930	intergenic_region ; MODIFIER	silent_mutation	Average:27.927; most accessible tissue: Zhenshan97 flag leaf, score: 41.874	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0723951270	3.59E-07	NA	mr1928	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
vg0723951270	2.01E-06	1.61E-06	mr1928	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
vg0723951270	NA	3.07E-06	mr1181_2	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