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Detailed information for vg1120801482:

Variant ID: vg1120801482 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20801482
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, T: 0.09, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTTTCTTTCGAGATAATCCATTATATGCCATTAACTTTATCGCACGTCTACGATTTGCCACTGACTTTGTCACGTTCTACAATATGCCATCGACTTTT[G/T]
CTTAACTTCTACGATTTACCATCGCCGTCCGGTTAACCACCTTTAGTACTGTACAAATTTGTTGAAATGACCAAAATACCCCTATGACAAAAATATCCAA

Reverse complement sequence

TTGGATATTTTTGTCATAGGGGTATTTTGGTCATTTCAACAAATTTGTACAGTACTAAAGGTGGTTAACCGGACGGCGATGGTAAATCGTAGAAGTTAAG[C/A]
AAAAGTCGATGGCATATTGTAGAACGTGACAAAGTCAGTGGCAAATCGTAGACGTGCGATAAAGTTAATGGCATATAATGGATTATCTCGAAAGAAAAAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.90%	39.50%	0.13%	2.45%	NA
All Indica	2759	33.50%	64.00%	0.18%	2.36%	NA
All Japonica	1512	95.10%	3.00%	0.00%	1.92%	NA
Aus	269	87.70%	5.20%	0.00%	7.06%	NA
Indica I	595	75.30%	24.40%	0.34%	0.00%	NA
Indica II	465	18.50%	78.90%	0.00%	2.58%	NA
Indica III	913	16.30%	80.00%	0.00%	3.72%	NA
Indica Intermediate	786	30.70%	66.50%	0.38%	2.42%	NA
Temperate Japonica	767	96.30%	3.50%	0.00%	0.13%	NA
Tropical Japonica	504	92.30%	2.60%	0.00%	5.16%	NA
Japonica Intermediate	241	97.10%	2.10%	0.00%	0.83%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	63.30%	32.20%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120801482	G -> T	LOC_Os11g35500.1	upstream_gene_variant ; 1442.0bp to feature; MODIFIER	silent_mutation	Average:42.237; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg1120801482	G -> T	LOC_Os11g35490.1	downstream_gene_variant ; 2043.0bp to feature; MODIFIER	silent_mutation	Average:42.237; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg1120801482	G -> T	LOC_Os11g35490-LOC_Os11g35500	intergenic_region ; MODIFIER	silent_mutation	Average:42.237; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg1120801482	G -> DEL	N	N	silent_mutation	Average:42.237; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120801482	NA	5.03E-06	mr1324	Jap_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
vg1120801482	NA	6.64E-06	mr1341_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
vg1120801482	NA	3.94E-06	mr1557_2	Jap_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
vg1120801482	4.45E-06	4.08E-07	mr1623_2	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
vg1120801482	NA	9.63E-06	mr1779_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