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Detailed information for vg0720903383:

Variant ID: vg0720903383 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 20903383
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:

CGTGGTCGACCGAATTACCCCCTTTAACCCAAAAACCAAACATTGCTTACTCTGAACTTTTTTTTTTTAACGAAACTCACCCTGAACTTTCAATACCGGA[C/T]
GAATTACCCCCCTCGACTCAATCCCGAGCAGTTTCGTCTTACGTGGTGTACGCGTGGCAATCTAGTCAGCATTTTTTTTTTTAAAAAAAAGGGTGGGACC

Reverse complement sequence

GGTCCCACCCTTTTTTTTAAAAAAAAAAATGCTGACTAGATTGCCACGCGTACACCACGTAAGACGAAACTGCTCGGGATTGAGTCGAGGGGGGTAATTC[G/A]
TCCGGTATTGAAAGTTCAGGGTGAGTTTCGTTAAAAAAAAAAAGTTCAGAGTAAGCAATGTTTGGTTTTTGGGTTAAAGGGGGTAATTCGGTCGACCACG

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	80.80%	13.80%	0.21%	5.18%	NA
All Indica	2759	79.30%	19.30%	0.07%	1.27%	NA
All Japonica	1512	97.20%	1.50%	0.00%	1.39%	NA
Aus	269	30.90%	1.10%	2.60%	65.43%	NA
Indica I	595	89.70%	9.70%	0.00%	0.50%	NA
Indica II	465	80.40%	19.40%	0.00%	0.22%	NA
Indica III	913	70.50%	28.60%	0.00%	0.88%	NA
Indica Intermediate	786	81.00%	15.80%	0.25%	2.93%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	96.80%	0.80%	0.00%	2.38%	NA
Japonica Intermediate	241	90.00%	6.20%	0.00%	3.73%	NA
VI/Aromatic	96	11.50%	79.20%	1.04%	8.33%	NA
Intermediate	90	75.60%	18.90%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0720903383	C -> DEL	N	N	silent_mutation	Average:73.288; most accessible tissue: Zhenshan97 panicle, score: 89.389	N	N	N	N
vg0720903383	C -> T	LOC_Os07g34870.1	upstream_gene_variant ; 1639.0bp to feature; MODIFIER	silent_mutation	Average:73.288; most accessible tissue: Zhenshan97 panicle, score: 89.389	N	N	N	N
vg0720903383	C -> T	LOC_Os07g34880.1	upstream_gene_variant ; 830.0bp to feature; MODIFIER	silent_mutation	Average:73.288; most accessible tissue: Zhenshan97 panicle, score: 89.389	N	N	N	N
vg0720903383	C -> T	LOC_Os07g34870-LOC_Os07g34880	intergenic_region ; MODIFIER	silent_mutation	Average:73.288; most accessible tissue: Zhenshan97 panicle, score: 89.389	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0720903383	2.21E-06	NA	mr1792_2	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
vg0720903383	NA	7.08E-06	mr1968_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