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Detailed information for vg0905693969:

Variant ID: vg0905693969 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5693969
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTGTGGGAGCAAGGTTGGGCGTCTTCTTGGCAGCTACATTGTTGTTCTTCACCGAGTTCTTCGCGTTCTTCGTGTTCTTGAGGTACCCATCTTAAAATC[G/A]
AATCCCTCGATTCCTCGAGTTTAATCTTGCGATTTCCTTCGGTGGAGTTGTTCCCCTAGTGCCATAGACCCTGTAGATTCAATTTCACAAGTTTTTGTTG

Reverse complement sequence

CAACAAAAACTTGTGAAATTGAATCTACAGGGTCTATGGCACTAGGGGAACAACTCCACCGAAGGAAATCGCAAGATTAAACTCGAGGAATCGAGGGATT[C/T]
GATTTTAAGATGGGTACCTCAAGAACACGAAGAACGCGAAGAACTCGGTGAAGAACAACAATGTAGCTGCCAAGAAGACGCCCAACCTTGCTCCCACAAA

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	57.50%	24.30%	9.92%	8.32%	NA
All Indica	2759	41.40%	40.90%	16.27%	1.49%	NA
All Japonica	1512	82.20%	0.70%	0.40%	16.73%	NA
Aus	269	95.90%	0.00%	1.12%	2.97%	NA
Indica I	595	37.10%	41.50%	21.01%	0.34%	NA
Indica II	465	42.80%	39.10%	17.42%	0.65%	NA
Indica III	913	41.70%	45.00%	10.73%	2.52%	NA
Indica Intermediate	786	43.30%	36.60%	18.45%	1.65%	NA
Temperate Japonica	767	91.40%	0.80%	0.52%	7.30%	NA
Tropical Japonica	504	82.70%	0.00%	0.20%	17.06%	NA
Japonica Intermediate	241	51.90%	1.70%	0.41%	46.06%	NA
VI/Aromatic	96	15.60%	1.00%	3.12%	80.21%	NA
Intermediate	90	65.60%	10.00%	8.89%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0905693969	G -> DEL	N	N	silent_mutation	Average:29.581; most accessible tissue: Callus, score: 52.669	N	N	N	N
vg0905693969	G -> A	LOC_Os09g10430.1	upstream_gene_variant ; 3768.0bp to feature; MODIFIER	silent_mutation	Average:29.581; most accessible tissue: Callus, score: 52.669	N	N	N	N
vg0905693969	G -> A	LOC_Os09g10410.1	downstream_gene_variant ; 1351.0bp to feature; MODIFIER	silent_mutation	Average:29.581; most accessible tissue: Callus, score: 52.669	N	N	N	N
vg0905693969	G -> A	LOC_Os09g10420.1	downstream_gene_variant ; 2139.0bp to feature; MODIFIER	silent_mutation	Average:29.581; most accessible tissue: Callus, score: 52.669	N	N	N	N
vg0905693969	G -> A	LOC_Os09g10410-LOC_Os09g10420	intergenic_region ; MODIFIER	silent_mutation	Average:29.581; most accessible tissue: Callus, score: 52.669	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905693969	6.24E-06	7.44E-06	mr1682	Jap_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
vg0905693969	NA	6.18E-06	mr1759	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