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Detailed information for vg0702318162:

Variant ID: vg0702318162 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 2318162
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, A: 0.28, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

AGGTAGCTGGCCAAATGCAGGGGCAGCAAGCAGGAGCAGCACCAAAAAACTCCCAAGAATCCCCATTGCTGCTCTCCAGACAAAGATTGGAAGCTACTGA[G/A]
CCTCAAAGACACAGCACCTGAAGCATTTCTTGCAGCAAAAATGGACTGGAAGTGTAGAGTGTATCTACCAGAAGGCTCTCACAACAAGCTGCCACTAATA

Reverse complement sequence

TATTAGTGGCAGCTTGTTGTGAGAGCCTTCTGGTAGATACACTCTACACTTCCAGTCCATTTTTGCTGCAAGAAATGCTTCAGGTGCTGTGTCTTTGAGG[C/T]
TCAGTAGCTTCCAATCTTTGTCTGGAGAGCAGCAATGGGGATTCTTGGGAGTTTTTTGGTGCTGCTCCTGCTTGCTGCCCCTGCATTTGGCCAGCTACCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.70%	42.80%	0.25%	0.25%	NA
All Indica	2759	85.90%	13.40%	0.29%	0.43%	NA
All Japonica	1512	1.00%	99.00%	0.00%	0.00%	NA
Aus	269	88.10%	11.50%	0.37%	0.00%	NA
Indica I	595	93.80%	5.70%	0.34%	0.17%	NA
Indica II	465	50.10%	48.80%	0.22%	0.86%	NA
Indica III	913	98.60%	1.10%	0.00%	0.33%	NA
Indica Intermediate	786	86.30%	12.60%	0.64%	0.51%	NA
Temperate Japonica	767	0.10%	99.90%	0.00%	0.00%	NA
Tropical Japonica	504	2.80%	97.20%	0.00%	0.00%	NA
Japonica Intermediate	241	0.00%	100.00%	0.00%	0.00%	NA
VI/Aromatic	96	27.10%	72.90%	0.00%	0.00%	NA
Intermediate	90	35.60%	61.10%	3.33%	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
vg0702318162	G -> DEL	N	N	silent_mutation	Average:60.493; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg0702318162	G -> A	LOC_Os07g05190.1	5_prime_UTR_variant ; 35.0bp to feature; MODIFIER	silent_mutation	Average:60.493; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0702318162	NA	2.00E-09	mr1005	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
vg0702318162	NA	2.05E-14	mr1059	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
vg0702318162	NA	3.18E-15	mr1950	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
vg0702318162	NA	9.74E-10	mr1158_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
vg0702318162	NA	2.33E-10	mr1383_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
vg0702318162	NA	2.69E-07	mr1482_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
vg0702318162	NA	7.75E-08	mr1645_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