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Detailed information for vg1207943829:

Variant ID: vg1207943829 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7943829
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTGGGACGAGGCTCATGTGTTGGGCAGTCGCGGAGCGCGGGTAAAGTGTACATCCACTGCAGTGTGAGTAAAACAAATCTATTCGAATAGCCGTGCTC[G/A]
CGGTTATTGAGCACCGGAACATGTATTACACTTGGGTAGACTCTAAATTCTTAACTTGTGTGGGATGGGTTATTGCATGATGATTTTTATGCTGTTGGAG

Reverse complement sequence

CTCCAACAGCATAAAAATCATCATGCAATAACCCATCCCACACAAGTTAAGAATTTAGAGTCTACCCAAGTGTAATACATGTTCCGGTGCTCAATAACCG[C/T]
GAGCACGGCTATTCGAATAGATTTGTTTTACTCACACTGCAGTGGATGTACACTTTACCCGCGCTCCGCGACTGCCCAACACATGAGCCTCGTCCCAACA

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	56.30%	17.00%	0.91%	25.77%	NA
All Indica	2759	83.70%	3.00%	0.72%	12.61%	NA
All Japonica	1512	6.10%	43.80%	0.93%	49.21%	NA
Aus	269	67.70%	3.70%	1.49%	27.14%	NA
Indica I	595	79.00%	3.70%	0.34%	16.97%	NA
Indica II	465	88.80%	5.20%	0.43%	5.59%	NA
Indica III	913	87.20%	0.70%	0.77%	11.39%	NA
Indica Intermediate	786	80.20%	3.80%	1.15%	14.89%	NA
Temperate Japonica	767	7.00%	68.60%	0.65%	23.73%	NA
Tropical Japonica	504	5.80%	12.70%	1.59%	79.96%	NA
Japonica Intermediate	241	3.70%	29.90%	0.41%	65.98%	NA
VI/Aromatic	96	46.90%	21.90%	1.04%	30.21%	NA
Intermediate	90	36.70%	32.20%	4.44%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1207943829	G -> DEL	N	N	silent_mutation	Average:65.036; most accessible tissue: Minghui63 flag leaf, score: 85.67	N	N	N	N
vg1207943829	G -> A	LOC_Os12g13980.1	upstream_gene_variant ; 1973.0bp to feature; MODIFIER	silent_mutation	Average:65.036; most accessible tissue: Minghui63 flag leaf, score: 85.67	N	N	N	N
vg1207943829	G -> A	LOC_Os12g13980-LOC_Os12g13990	intergenic_region ; MODIFIER	silent_mutation	Average:65.036; most accessible tissue: Minghui63 flag leaf, score: 85.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207943829	NA	2.40E-07	mr1041_2	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
vg1207943829	NA	2.60E-06	mr1289_2	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
vg1207943829	NA	4.43E-07	mr1293_2	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
vg1207943829	NA	5.61E-07	mr1302_2	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
vg1207943829	NA	2.46E-07	mr1418_2	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
vg1207943829	NA	3.05E-06	mr1420_2	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
vg1207943829	NA	7.22E-06	mr1467_2	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
vg1207943829	3.67E-06	NA	mr1494_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
vg1207943829	NA	6.31E-06	mr1508_2	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
vg1207943829	NA	3.01E-09	mr1604_2	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
vg1207943829	NA	1.60E-08	mr1683_2	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
vg1207943829	NA	1.35E-08	mr1824_2	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
vg1207943829	NA	8.92E-14	mr1838_2	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