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Detailed information for vg1104601543:

Variant ID: vg1104601543 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4601543
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, A: 0.23, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

ACAGATGAGGCAGAAAAGTTGCAACAGAAAGGGCTACGTTCAGCAGTCTTGACCACACTTTGGGAGATTTGGATGGAAAGGAACAATCGCATCTTCAGAG[A/G]
GAAAGAATCTACAGCATCAGCACTTGCTAGCAAGATCATAGATGAGCTTCATTTGTGGAAAATGGCAGGTGCCAAGGGAGTGAAGTGTATTATGTTAATA

Reverse complement sequence

TATTAACATAATACACTTCACTCCCTTGGCACCTGCCATTTTCCACAAATGAAGCTCATCTATGATCTTGCTAGCAAGTGCTGATGCTGTAGATTCTTTC[T/C]
CTCTGAAGATGCGATTGTTCCTTTCCATCCAAATCTCCCAAAGTGTGGTCAAGACTGCTGAACGTAGCCCTTTCTGTTGCAACTTTTCTGCCTCATCTGT

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	59.00%	40.80%	0.17%	0.00%	NA
All Indica	2759	52.30%	47.40%	0.25%	0.00%	NA
All Japonica	1512	74.90%	25.00%	0.07%	0.00%	NA
Aus	269	29.40%	70.60%	0.00%	0.00%	NA
Indica I	595	17.80%	81.50%	0.67%	0.00%	NA
Indica II	465	81.10%	18.90%	0.00%	0.00%	NA
Indica III	913	55.50%	44.50%	0.00%	0.00%	NA
Indica Intermediate	786	57.80%	41.90%	0.38%	0.00%	NA
Temperate Japonica	767	59.30%	40.50%	0.13%	0.00%	NA
Tropical Japonica	504	95.00%	5.00%	0.00%	0.00%	NA
Japonica Intermediate	241	82.60%	17.40%	0.00%	0.00%	NA
VI/Aromatic	96	67.70%	32.30%	0.00%	0.00%	NA
Intermediate	90	74.40%	25.60%	0.00%	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
vg1104601543	A -> G	LOC_Os11g08640.1	downstream_gene_variant ; 499.0bp to feature; MODIFIER	silent_mutation	Average:53.175; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg1104601543	A -> G	LOC_Os11g08640-LOC_Os11g08650	intergenic_region ; MODIFIER	silent_mutation	Average:53.175; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104601543	NA	4.04E-06	mr1174	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
vg1104601543	NA	2.57E-06	mr1347	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
vg1104601543	NA	2.88E-10	mr1050_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
vg1104601543	NA	6.91E-06	mr1050_2	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
vg1104601543	NA	3.83E-08	mr1272_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
vg1104601543	NA	1.22E-06	mr1531_2	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
vg1104601543	NA	2.19E-07	mr1624_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
vg1104601543	NA	2.26E-06	mr1788_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
vg1104601543	NA	3.37E-10	mr1887_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
vg1104601543	NA	3.28E-07	mr1887_2	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