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Detailed information for vg0800263929:

Variant ID: vg0800263929 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 263929
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATGCCGTTAAATCCTGAAAAATTTGCTCCCATGGGAAGTCAAACCCAGGATCTAAGGTGCTATTGAGACTCCTGTAACTACTAGGTTACAGGCCCTTTC[G/A]
CAAACTCGACTATCCTTAGTTGAATACTCTCCACAAAATTCGATCTAAAATTTAAAATTATGACAATCAATTTTATATTAAAATAAGTTGATAGGTCTGG

Reverse complement sequence

CCAGACCTATCAACTTATTTTAATATAAAATTGATTGTCATAATTTTAAATTTTAGATCGAATTTTGTGGAGAGTATTCAACTAAGGATAGTCGAGTTTG[C/T]
GAAAGGGCCTGTAACCTAGTAGTTACAGGAGTCTCAATAGCACCTTAGATCCTGGGTTTGACTTCCCATGGGAGCAAATTTTTCAGGATTTAACGGCATT

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	98.40%	0.90%	0.72%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.07%	0.00%	NA
All Japonica	1512	95.20%	2.70%	2.12%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	92.80%	4.30%	2.87%	0.00%	NA
Tropical Japonica	504	98.60%	0.40%	0.99%	0.00%	NA
Japonica Intermediate	241	95.40%	2.50%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0800263929	G -> A	LOC_Os08g01400.1	upstream_gene_variant ; 2609.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800263929	G -> A	LOC_Os08g01410.1	downstream_gene_variant ; 4787.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800263929	G -> A	LOC_Os08g01400-LOC_Os08g01410	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0800263929	2.23E-07	2.23E-07	mr1412	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