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Detailed information for vg0807824555:

Variant ID: vg0807824555 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7824555
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCACGATCGTAGCACCTTAAGCCTTGCGGTGATTCTAGAGTCGCCAACCACCTCGATCTAGCAAAGAGCTAAATCTAGATGGGTTTTGATAACTAAACC[G/A]
GCTAGCGGAGCCGATTTCTAGATAACTACCTGTCTCATGGGCAAAACAGAAGGTTTTCAGGACAAACATACAAAGAGATGTCGCACTCTCGCAGCGGCGG

Reverse complement sequence

CCGCCGCTGCGAGAGTGCGACATCTCTTTGTATGTTTGTCCTGAAAACCTTCTGTTTTGCCCATGAGACAGGTAGTTATCTAGAAATCGGCTCCGCTAGC[C/T]
GGTTTAGTTATCAAAACCCATCTAGATTTAGCTCTTTGCTAGATCGAGGTGGTTGGCGACTCTAGAATCACCGCAAGGCTTAAGGTGCTACGATCGTGCT

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	95.70%	2.50%	0.21%	1.63%	NA
All Indica	2759	96.90%	0.00%	0.33%	2.75%	NA
All Japonica	1512	92.60%	7.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.00%	0.17%	NA
Indica II	465	98.30%	0.00%	0.22%	1.51%	NA
Indica III	913	92.30%	0.10%	0.88%	6.68%	NA
Indica Intermediate	786	99.10%	0.00%	0.00%	0.89%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	94.40%	5.60%	0.00%	0.00%	NA
Japonica Intermediate	241	68.00%	32.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	96.70%	1.10%	1.11%	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
vg0807824555	G -> A	LOC_Os08g13160.1	downstream_gene_variant ; 3907.0bp to feature; MODIFIER	silent_mutation	Average:38.995; most accessible tissue: Callus, score: 55.732	N	N	N	N
vg0807824555	G -> A	LOC_Os08g13170.1	downstream_gene_variant ; 586.0bp to feature; MODIFIER	silent_mutation	Average:38.995; most accessible tissue: Callus, score: 55.732	N	N	N	N
vg0807824555	G -> A	LOC_Os08g13160-LOC_Os08g13170	intergenic_region ; MODIFIER	silent_mutation	Average:38.995; most accessible tissue: Callus, score: 55.732	N	N	N	N
vg0807824555	G -> DEL	N	N	silent_mutation	Average:38.995; most accessible tissue: Callus, score: 55.732	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0807824555	NA	2.08E-06	mr1123	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
vg0807824555	NA	5.15E-06	mr1242	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
vg0807824555	1.12E-06	NA	mr1757	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
vg0807824555	NA	2.36E-06	mr1961	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