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Detailed information for vg0703429520:

Variant ID: vg0703429520 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 3429520
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, C: 0.25, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTTTTTTAAAAAAACACATTATTTAGCTATTCGGAAAATACGCACGTGGAAAACAAGATTGGTGAAATTGGCAACATTGACTTTAGAACACAGCCCAA[G/C]
GCATTAACCCACCAACATCCGGGGACACGATCTTGAGTTGAGTTTCCTACTGACGACAAGTTAATGCCAACTACAGTACTAATCAGAATCTCCATCTCAG

Reverse complement sequence

CTGAGATGGAGATTCTGATTAGTACTGTAGTTGGCATTAACTTGTCGTCAGTAGGAAACTCAACTCAAGATCGTGTCCCCGGATGTTGGTGGGTTAATGC[C/G]
TTGGGCTGTGTTCTAAAGTCAATGTTGCCAATTTCACCAATCTTGTTTTCCACGTGCGTATTTTCCGAATAGCTAAATAATGTGTTTTTTTAAAAAAAAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.90%	43.60%	0.08%	0.38%	NA
All Indica	2759	35.70%	63.60%	0.04%	0.58%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	3.30%	96.70%	0.00%	0.00%	NA
Indica I	595	84.70%	15.00%	0.00%	0.34%	NA
Indica II	465	15.10%	84.10%	0.00%	0.86%	NA
Indica III	913	16.00%	83.70%	0.00%	0.33%	NA
Indica Intermediate	786	33.80%	65.10%	0.13%	0.89%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	60.00%	34.40%	3.33%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0703429520	G -> DEL	N	N	silent_mutation	Average:68.249; most accessible tissue: Callus, score: 93.643	N	N	N	N
vg0703429520	G -> C	LOC_Os07g06970.1	3_prime_UTR_variant ; 155.0bp to feature; MODIFIER	silent_mutation	Average:68.249; most accessible tissue: Callus, score: 93.643	N	N	N	N
vg0703429520	G -> C	LOC_Os07g06960.1	upstream_gene_variant ; 1053.0bp to feature; MODIFIER	silent_mutation	Average:68.249; most accessible tissue: Callus, score: 93.643	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0703429520	NA	3.63E-07	mr1291	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
vg0703429520	NA	9.57E-06	mr1531	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
vg0703429520	NA	1.29E-17	mr1557	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
vg0703429520	NA	9.18E-06	mr1679	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
vg0703429520	NA	6.89E-06	mr1904	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
vg0703429520	NA	7.72E-06	mr1974_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