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Detailed information for vg1006275829:

Variant ID: vg1006275829 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 6275829
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:

AAATGTTGTGCTCATTAAATCTTTATATGTGTTGAGTGTTGTGTACATGCAGGGAATATATGCAAAGTGACTGAATGTGTAGCGGGATCTTTGTACGAAT[A/G]
AATACTCAAAACTTGTACTGATTCAAACTGATTCGATGAACCAAGTATTTATTTACTATCATCAAACTTATCCGGGGTATTCGATCATTGAACTAAGGTA

Reverse complement sequence

TACCTTAGTTCAATGATCGAATACCCCGGATAAGTTTGATGATAGTAAATAAATACTTGGTTCATCGAATCAGTTTGAATCAGTACAAGTTTTGAGTATT[T/C]
ATTCGTACAAAGATCCCGCTACACATTCAGTCACTTTGCATATATTCCCTGCATGTACACAACACTCAACACATATAAAGATTTAATGAGCACAACATTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.30%	3.50%	1.16%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	85.80%	10.50%	3.64%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	73.10%	20.20%	6.65%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	1.70%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg1006275829	A -> G	LOC_Os10g11310.1	intron_variant ; MODIFIER	silent_mutation	Average:59.946; most accessible tissue: Zhenshan97 young leaf, score: 77.422	N	N	N	N
vg1006275829	A -> G	LOC_Os10g11310.2	intron_variant ; MODIFIER	silent_mutation	Average:59.946; most accessible tissue: Zhenshan97 young leaf, score: 77.422	N	N	N	N
vg1006275829	A -> G	LOC_Os10g11310.3	intron_variant ; MODIFIER	silent_mutation	Average:59.946; most accessible tissue: Zhenshan97 young leaf, score: 77.422	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1006275829	4.27E-06	NA	mr1310_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
vg1006275829	7.37E-06	5.86E-07	mr1959_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