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Detailed information for vg0819245930:

Variant ID: vg0819245930 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19245930
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCGGCCACGACTACTGCTCCCTCTTATACAAGGGGTGTGGTGCGCTAGTGCGTGAACCAGACTGCGCCGGTGGCAGGAGAGGAGGCCGACAAGGATGTC[G/A]
GTGGTGGGCACATTGATAGGGTAGCAGGCGCGTCTCGATGGGTCAGTGACGGCGAGCTTCACGGTGGTGCCATGGTTGCGGAAGAGTAGGAGGTGGACAC

Reverse complement sequence

GTGTCCACCTCCTACTCTTCCGCAACCATGGCACCACCGTGAAGCTCGCCGTCACTGACCCATCGAGACGCGCCTGCTACCCTATCAATGTGCCCACCAC[C/T]
GACATCCTTGTCGGCCTCCTCTCCTGCCACCGGCGCAGTCTGGTTCACGCACTAGCGCACCACACCCCTTGTATAAGAGGGAGCAGTAGTCGTGGCCGGA

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	94.70%	4.70%	0.66%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	87.90%	10.30%	1.85%	0.00%	NA
Aus	269	96.70%	3.30%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	91.10%	6.50%	2.35%	0.00%	NA
Tropical Japonica	504	94.80%	5.20%	0.00%	0.00%	NA
Japonica Intermediate	241	63.10%	32.80%	4.15%	0.00%	NA
VI/Aromatic	96	55.20%	42.70%	2.08%	0.00%	NA
Intermediate	90	84.40%	14.40%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0819245930	G -> A	LOC_Os08g31140.1	downstream_gene_variant ; 170.0bp to feature; MODIFIER	silent_mutation	Average:75.849; most accessible tissue: Zhenshan97 young leaf, score: 90.27	N	N	N	N
vg0819245930	G -> A	LOC_Os08g31150.1	downstream_gene_variant ; 3713.0bp to feature; MODIFIER	silent_mutation	Average:75.849; most accessible tissue: Zhenshan97 young leaf, score: 90.27	N	N	N	N
vg0819245930	G -> A	LOC_Os08g31140-LOC_Os08g31150	intergenic_region ; MODIFIER	silent_mutation	Average:75.849; most accessible tissue: Zhenshan97 young leaf, score: 90.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819245930	6.92E-06	3.61E-07	mr1855_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