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Detailed information for vg1205533146:

Variant ID: vg1205533146 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5533146
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

AGAAGTCGCCAAGGAATCGCCTTTACGCCTAGGAATCGCCTTTATGCCAGAGGAATCGCCGGGGAAGAGAGAGAAAAAGTTTCGCTTGAGCGGTGAAAAC[G/A]
GAGGTCATGGCGTGAGATTTCTCGGGGGTAACGGTTAGTATTTAAAGCGCTGGAATAACGGTCAAAAGTGGCGGAGTGCGAAACTTGCTCGGAGTCGGCT

Reverse complement sequence

AGCCGACTCCGAGCAAGTTTCGCACTCCGCCACTTTTGACCGTTATTCCAGCGCTTTAAATACTAACCGTTACCCCCGAGAAATCTCACGCCATGACCTC[C/T]
GTTTTCACCGCTCAAGCGAAACTTTTTCTCTCTCTTCCCCGGCGATTCCTCTGGCATAAAGGCGATTCCTAGGCGTAAAGGCGATTCCTTGGCGACTTCT

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	56.30%	39.30%	1.02%	3.36%	NA
All Indica	2759	30.60%	66.10%	0.83%	2.46%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	58.00%	1.50%	8.55%	31.97%	NA
Indica I	595	72.80%	25.40%	0.67%	1.18%	NA
Indica II	465	20.20%	78.70%	0.65%	0.43%	NA
Indica III	913	5.80%	90.40%	0.99%	2.85%	NA
Indica Intermediate	786	33.60%	61.30%	0.89%	4.20%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	98.00%	2.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	0.00%	1.04%	NA
Intermediate	90	74.40%	18.90%	2.22%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1205533146	G -> DEL	N	N	silent_mutation	Average:47.948; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg1205533146	G -> A	LOC_Os12g10430.1	downstream_gene_variant ; 3777.0bp to feature; MODIFIER	silent_mutation	Average:47.948; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg1205533146	G -> A	LOC_Os12g10440.1	intron_variant ; MODIFIER	silent_mutation	Average:47.948; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1205533146	NA	3.67E-06	mr1030	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
vg1205533146	NA	5.73E-07	mr1057	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
vg1205533146	NA	1.92E-06	mr1285	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
vg1205533146	NA	1.74E-08	mr1301	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
vg1205533146	3.57E-06	1.30E-07	mr1511	Ind_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
vg1205533146	NA	9.32E-06	mr1656	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
vg1205533146	4.54E-06	4.55E-06	mr1673	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
vg1205533146	NA	1.81E-07	mr1527_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