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Detailed information for vg0335235562:

Variant ID: vg0335235562 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35235562
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGAATCATAATAACATTCTATTATCCTTTACCTAATCCTAGAACGAGCTTATTTTCTTTAGCTCCGATAAATGTTCAATGGTAATCATGGCCACCTCAAA[G/A]
AACTATAGCTTATAGCAACGATGTGAAGGTATACAATTTTTTTTACGTTTAATATAAAACAAATCACTACACCAGGATACAATTTTTTTTGTTGTTAAAT

Reverse complement sequence

ATTTAACAACAAAAAAAATTGTATCCTGGTGTAGTGATTTGTTTTATATTAAACGTAAAAAAAATTGTATACCTTCACATCGTTGCTATAAGCTATAGTT[C/T]
TTTGAGGTGGCCATGATTACCATTGAACATTTATCGGAGCTAAAGAAAATAAGCTCGTTCTAGGATTAGGTAAAGGATAATAGAATGTTATTATGATTCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.20%	2.70%	1.76%	20.33%	NA
All Indica	2759	64.50%	0.30%	1.12%	34.11%	NA
All Japonica	1512	88.60%	7.70%	3.44%	0.20%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	58.50%	0.70%	1.34%	39.50%	NA
Indica II	465	75.10%	0.00%	0.86%	24.09%	NA
Indica III	913	57.50%	0.00%	1.42%	41.07%	NA
Indica Intermediate	786	71.00%	0.40%	0.76%	27.86%	NA
Temperate Japonica	767	80.30%	13.30%	6.39%	0.00%	NA
Tropical Japonica	504	99.00%	0.40%	0.00%	0.60%	NA
Japonica Intermediate	241	93.40%	5.40%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	78.90%	2.20%	0.00%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0335235562	G -> A	LOC_Os03g62200.1	upstream_gene_variant ; 2693.0bp to feature; MODIFIER	silent_mutation	Average:31.495; most accessible tissue: Callus, score: 87.323	N	N	N	N
vg0335235562	G -> A	LOC_Os03g62190.1	downstream_gene_variant ; 4619.0bp to feature; MODIFIER	silent_mutation	Average:31.495; most accessible tissue: Callus, score: 87.323	N	N	N	N
vg0335235562	G -> A	LOC_Os03g62190-LOC_Os03g62200	intergenic_region ; MODIFIER	silent_mutation	Average:31.495; most accessible tissue: Callus, score: 87.323	N	N	N	N
vg0335235562	G -> DEL	N	N	silent_mutation	Average:31.495; most accessible tissue: Callus, score: 87.323	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0335235562	2.93E-06	NA	mr1024	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
vg0335235562	NA	3.15E-08	mr1062	Jap_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
vg0335235562	4.99E-08	NA	mr1024_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
vg0335235562	5.81E-06	5.81E-06	mr1024_2	Jap_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
vg0335235562	NA	9.18E-07	mr1062_2	Jap_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
vg0335235562	NA	2.07E-06	mr1565_2	Jap_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
vg0335235562	NA	7.12E-06	mr1913_2	Jap_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