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Detailed information for vg0707039898:

Variant ID: vg0707039898 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 7039898
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, A: 0.35, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

GCGTCTGATTAATTAAGTATTAGCTATTTTTAAAAAAAATAGATTAATTTGATTTTTTTAAGCAACTTTCGTTTAGAAACTTTTTGCAAAAAAATATATT[A/G]
TTTAGCAGTTTGAAAAGCGTGCGTGTGAAGAACTATAGAGAGGGGTTGGGAAGTGGCTGAAACGAACGAAGCCAGGTGATGGAGTTCATATATAGTACCT

Reverse complement sequence

AGGTACTATATATGAACTCCATCACCTGGCTTCGTTCGTTTCAGCCACTTCCCAACCCCTCTCTATAGTTCTTCACACGCACGCTTTTCAAACTGCTAAA[T/C]
AATATATTTTTTTGCAAAAAGTTTCTAAACGAAAGTTGCTTAAAAAAATCAAATTAATCTATTTTTTTTAAAAATAGCTAATACTTAATTAATCAGACGC

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	61.00%	35.60%	0.49%	2.94%	NA
All Indica	2759	90.80%	3.70%	0.76%	4.78%	NA
All Japonica	1512	13.90%	86.00%	0.13%	0.00%	NA
Aus	269	39.80%	58.00%	0.00%	2.23%	NA
Indica I	595	97.50%	1.00%	0.67%	0.84%	NA
Indica II	465	82.80%	7.50%	1.94%	7.74%	NA
Indica III	913	91.80%	1.00%	0.22%	7.01%	NA
Indica Intermediate	786	89.30%	6.50%	0.76%	3.44%	NA
Temperate Japonica	767	4.60%	95.20%	0.26%	0.00%	NA
Tropical Japonica	504	13.70%	86.30%	0.00%	0.00%	NA
Japonica Intermediate	241	44.00%	56.00%	0.00%	0.00%	NA
VI/Aromatic	96	14.60%	85.40%	0.00%	0.00%	NA
Intermediate	90	50.00%	48.90%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0707039898	A -> DEL	N	N	silent_mutation	Average:59.603; most accessible tissue: Callus, score: 85.18	N	N	N	N
vg0707039898	A -> G	LOC_Os07g12370.1	upstream_gene_variant ; 3356.0bp to feature; MODIFIER	silent_mutation	Average:59.603; most accessible tissue: Callus, score: 85.18	N	N	N	N
vg0707039898	A -> G	LOC_Os07g12370-LOC_Os07g12380	intergenic_region ; MODIFIER	silent_mutation	Average:59.603; most accessible tissue: Callus, score: 85.18	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0707039898	NA	2.67E-10	mr1195	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
vg0707039898	NA	1.22E-09	mr1379	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
vg0707039898	NA	1.52E-21	mr1416	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
vg0707039898	NA	1.50E-06	mr1203_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
vg0707039898	NA	4.16E-09	mr1379_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
vg0707039898	4.32E-06	3.06E-06	mr1402_2	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
vg0707039898	6.08E-06	NA	mr1613_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
vg0707039898	4.56E-06	2.89E-06	mr1613_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