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Detailed information for vg0621355218:

Variant ID: vg0621355218 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 21355218
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

ACTATGCCATCAGCTTTGCATTACTTAGGTGACGACTCCCTTGTATTTTGCCACCATTGATGCCTCCACGGCCGGTTATCCACTTTAGATCCACTACACC[A/G]
CTGCCAGCCTCACCACACCTCCCCAATCTCTCCCAACATAAAAAAAACAATTTCCTAGTCACTAGGAACGCATGATGACACCCTTGGAAGCCTGAGATCC

Reverse complement sequence

GGATCTCAGGCTTCCAAGGGTGTCATCATGCGTTCCTAGTGACTAGGAAATTGTTTTTTTTATGTTGGGAGAGATTGGGGAGGTGTGGTGAGGCTGGCAG[T/C]
GGTGTAGTGGATCTAAAGTGGATAACCGGCCGTGGAGGCATCAATGGTGGCAAAATACAAGGGAGTCGTCACCTAAGTAATGCAAAGCTGATGGCATAGT

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	68.60%	31.30%	0.06%	0.02%	NA
All Indica	2759	98.90%	1.00%	0.04%	0.04%	NA
All Japonica	1512	7.70%	92.30%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.10%	0.00%	0.11%	NA
Indica Intermediate	786	98.00%	2.00%	0.00%	0.00%	NA
Temperate Japonica	767	5.20%	94.80%	0.00%	0.00%	NA
Tropical Japonica	504	12.30%	87.50%	0.20%	0.00%	NA
Japonica Intermediate	241	5.80%	94.20%	0.00%	0.00%	NA
VI/Aromatic	96	78.10%	21.90%	0.00%	0.00%	NA
Intermediate	90	60.00%	38.90%	1.11%	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
vg0621355218	A -> G	LOC_Os06g36360.1	upstream_gene_variant ; 4825.0bp to feature; MODIFIER	silent_mutation	Average:75.117; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N
vg0621355218	A -> G	LOC_Os06g36370.1	downstream_gene_variant ; 1979.0bp to feature; MODIFIER	silent_mutation	Average:75.117; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N
vg0621355218	A -> G	LOC_Os06g36370-LOC_Os06g36380	intergenic_region ; MODIFIER	silent_mutation	Average:75.117; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N
vg0621355218	A -> DEL	N	N	silent_mutation	Average:75.117; most accessible tissue: Zhenshan97 panicle, score: 85.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0621355218	NA	5.91E-13	mr1010	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
vg0621355218	NA	4.26E-56	mr1019	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
vg0621355218	NA	6.47E-80	mr1134	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
vg0621355218	NA	1.30E-09	mr1198	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
vg0621355218	3.33E-07	3.33E-07	mr1267	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
vg0621355218	NA	7.20E-07	mr1690	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
vg0621355218	NA	2.10E-58	mr1695	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
vg0621355218	NA	5.50E-10	mr1714	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
vg0621355218	NA	5.01E-37	mr1719	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
vg0621355218	NA	5.64E-07	mr1979	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
vg0621355218	NA	6.74E-15	mr1148_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
vg0621355218	NA	7.00E-21	mr1276_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
vg0621355218	NA	1.10E-14	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
vg0621355218	NA	8.70E-07	mr1369_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
vg0621355218	NA	2.07E-07	mr1453_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
vg0621355218	NA	3.57E-10	mr1646_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
vg0621355218	NA	6.33E-09	mr1660_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