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Detailed information for vg0703513223:

Variant ID: vg0703513223 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 3513223
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

GATAGTGCCTCCGGATCTTCAAAGCATGAACCACTGCTGCCAATTCCAGGTCATGAGTTGGATAATTCCCTTCGTGTGGACGCAACTGTCGCGAGGCATA[C/T]
GCAACCACTCTGCCCTCTTGCATTAGGACACATCCAAGTCCGTGGCGGGATGCATCGCAATAGACTTGGAAGTCTTTCATCTGGTCGGGCAGAATCAAAA

Reverse complement sequence

TTTTGATTCTGCCCGACCAGATGAAAGACTTCCAAGTCTATTGCGATGCATCCCGCCACGGACTTGGATGTGTCCTAATGCAAGAGGGCAGAGTGGTTGC[G/A]
TATGCCTCGCGACAGTTGCGTCCACACGAAGGGAATTATCCAACTCATGACCTGGAATTGGCAGCAGTGGTTCATGCTTTGAAGATCCGGAGGCACTATC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.40%	7.60%	0.00%	0.00%	NA
All Indica	2759	93.90%	6.10%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	33.10%	66.90%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	94.80%	5.20%	0.00%	0.00%	NA
Indica III	913	87.80%	12.20%	0.00%	0.00%	NA
Indica Intermediate	786	95.90%	4.10%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg0703513223	C -> T	LOC_Os07g07130.1	upstream_gene_variant ; 970.0bp to feature; MODIFIER	silent_mutation	Average:36.239; most accessible tissue: Zhenshan97 flag leaf, score: 84.585	N	N	N	N
vg0703513223	C -> T	LOC_Os07g07094.1	downstream_gene_variant ; 1222.0bp to feature; MODIFIER	silent_mutation	Average:36.239; most accessible tissue: Zhenshan97 flag leaf, score: 84.585	N	N	N	N
vg0703513223	C -> T	LOC_Os07g07094-LOC_Os07g07130	intergenic_region ; MODIFIER	silent_mutation	Average:36.239; most accessible tissue: Zhenshan97 flag leaf, score: 84.585	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0703513223	NA	1.45E-08	mr1442	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
vg0703513223	NA	4.78E-07	mr1762	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