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Detailed information for vg1000967617:

Variant ID: vg1000967617 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 967617
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

AAGCTGGTTGATGGAAGATATGTTGTTTCCATTCACCCCACCATCTGTCAAAGTTCCAGCTCCTGAGCCTTGCCAGCTCTATGTTCTCAATACTGCCCAA[G/A]
GGGGGTCCTGGGATGTTGAGTAGCCGATCCATCATCAGAGTTGATGAAATTTCTCCTCGGCACTGGATTTTGTCAGCAAAGAATAAGCCGATTGGGAGTT

Reverse complement sequence

AACTCCCAATCGGCTTATTCTTTGCTGACAAAATCCAGTGCCGAGGAGAAATTTCATCAACTCTGATGATGGATCGGCTACTCAACATCCCAGGACCCCC[C/T]
TTGGGCAGTATTGAGAACATAGAGCTGGCAAGGCTCAGGAGCTGGAACTTTGACAGATGGTGGGGTGAATGGAAACAACATATCTTCCATCAACCAGCTT

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	39.00%	33.10%	2.52%	25.35%	NA
All Indica	2759	63.10%	2.20%	3.26%	31.50%	NA
All Japonica	1512	4.10%	90.00%	0.66%	5.22%	NA
Aus	269	8.90%	3.30%	4.46%	83.27%	NA
Indica I	595	22.20%	2.90%	4.03%	70.92%	NA
Indica II	465	88.40%	1.50%	0.86%	9.25%	NA
Indica III	913	77.80%	0.80%	2.96%	18.51%	NA
Indica Intermediate	786	62.00%	3.70%	4.45%	29.90%	NA
Temperate Japonica	767	0.70%	97.80%	0.39%	1.17%	NA
Tropical Japonica	504	9.70%	82.30%	1.19%	6.75%	NA
Japonica Intermediate	241	3.30%	81.30%	0.41%	14.94%	NA
VI/Aromatic	96	6.20%	88.50%	1.04%	4.17%	NA
Intermediate	90	12.20%	56.70%	6.67%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000967617	G -> A	LOC_Os10g02560.1	synonymous_variant ; p.Pro312Pro; LOW	synonymous_codon	Average:10.111; most accessible tissue: Callus, score: 30.081	N	N	N	N
vg1000967617	G -> A	LOC_Os10g02560.1	synonymous_variant ; p.Pro312Pro; LOW	nonsynonymous_codon ; P312S	Average:10.111; most accessible tissue: Callus, score: 30.081	benign	0.852	DELETERIOUS	0.05
vg1000967617	G -> DEL	LOC_Os10g02560.1	N	frameshift_variant	Average:10.111; most accessible tissue: Callus, score: 30.081	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000967617	NA	2.88E-07	mr1527	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
vg1000967617	NA	4.43E-11	mr1623	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
vg1000967617	NA	1.75E-11	mr1322_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
vg1000967617	NA	6.23E-17	mr1324_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
vg1000967617	NA	4.29E-13	mr1325_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
vg1000967617	NA	1.32E-16	mr1326_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
vg1000967617	NA	1.14E-14	mr1333_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
vg1000967617	NA	2.18E-19	mr1336_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
vg1000967617	NA	1.34E-08	mr1449_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
vg1000967617	NA	2.16E-08	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
vg1000967617	NA	5.91E-08	mr1623_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
vg1000967617	NA	2.44E-08	mr1690_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
vg1000967617	NA	1.03E-16	mr1744_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