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Detailed information for vg0507108976:

Variant ID: vg0507108976 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7108976
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

CATCTTTGTGGCCAGCCTCCTGATTATTCTAATCTGCGTCTTTTCGGTTGTGCTTGCTATGTGCTTCTTGCACCACGTGAGCGTACAAAGTTGACGGCTT[A/G]
GTCTGTTGAGTGTGTTTTTCTGGGTATAGTGCTGAACATAAGGGTTATCGTTGTTGGGATCCTGTAGGACGGCGGATGCGGATTTCACGGGATGTTACTT

Reverse complement sequence

AAGTAACATCCCGTGAAATCCGCATCCGCCGTCCTACAGGATCCCAACAACGATAACCCTTATGTTCAGCACTATACCCAGAAAAACACACTCAACAGAC[T/C]
AAGCCGTCAACTTTGTACGCTCACGTGGTGCAAGAAGCACATAGCAAGCACAACCGAAAAGACGCAGATTAGAATAATCAGGAGGCTGGCCACAAAGATG

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	75.20%	2.40%	17.25%	5.18%	NA
All Indica	2759	60.20%	2.60%	28.31%	8.81%	NA
All Japonica	1512	99.70%	0.10%	0.20%	0.00%	NA
Aus	269	79.90%	12.30%	7.81%	0.00%	NA
Indica I	595	43.50%	1.70%	42.86%	11.93%	NA
Indica II	465	81.90%	1.50%	11.40%	5.16%	NA
Indica III	913	64.20%	2.40%	25.08%	8.32%	NA
Indica Intermediate	786	55.50%	4.30%	31.04%	9.16%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	4.40%	11.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0507108976	A -> DEL	N	N	silent_mutation	Average:36.159; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N
vg0507108976	A -> G	LOC_Os05g12370.1	upstream_gene_variant ; 4208.0bp to feature; MODIFIER	silent_mutation	Average:36.159; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N
vg0507108976	A -> G	LOC_Os05g12360.1	intron_variant ; MODIFIER	silent_mutation	Average:36.159; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507108976	NA	9.69E-06	mr1409	Ind_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
vg0507108976	NA	5.06E-06	mr1531	Ind_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
vg0507108976	4.43E-06	NA	mr1593_2	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
vg0507108976	NA	5.02E-09	mr1593_2	Ind_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