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Detailed information for vg1125954146:

Variant ID: vg1125954146 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25954146
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTCTTGTATTTTTTTTCATAATATTTGTGGTACTACGATTTAAGCTAGGGTTAATTAATCGGATCGAAGCCACTACAAATATACCAAATTAGAAAAAT[G/A]
CTATTAATATTCGTGATATCAGATGGGTGTCACTGGAATTTAGAGAAATTGAAACCGTGCTACTCCGTCGCGTTTTCTATCCATCAGGGACGAAGCTATA

Reverse complement sequence

TATAGCTTCGTCCCTGATGGATAGAAAACGCGACGGAGTAGCACGGTTTCAATTTCTCTAAATTCCAGTGACACCCATCTGATATCACGAATATTAATAG[C/T]
ATTTTTCTAATTTGGTATATTTGTAGTGGCTTCGATCCGATTAATTAACCCTAGCTTAAATCGTAGTACCACAAATATTATGAAAAAAAATACAAGAAAT

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	92.80%	4.80%	0.38%	2.05%	NA
All Indica	2759	94.30%	5.50%	0.25%	0.00%	NA
All Japonica	1512	88.60%	4.60%	0.33%	6.42%	NA
Aus	269	97.00%	1.10%	1.86%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	98.90%	0.90%	0.22%	0.00%	NA
Indica III	913	87.60%	12.30%	0.11%	0.00%	NA
Indica Intermediate	786	95.80%	3.60%	0.64%	0.00%	NA
Temperate Japonica	767	81.10%	7.30%	0.65%	10.95%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	90.00%	4.60%	0.00%	5.39%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg1125954146	G -> A	LOC_Os11g43040.1	downstream_gene_variant ; 1907.0bp to feature; MODIFIER	silent_mutation	Average:42.794; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N
vg1125954146	G -> A	LOC_Os11g43040-LOC_Os11g43060	intergenic_region ; MODIFIER	silent_mutation	Average:42.794; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N
vg1125954146	G -> DEL	N	N	silent_mutation	Average:42.794; most accessible tissue: Minghui63 root, score: 70.803	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125954146	NA	6.95E-06	mr1280	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
vg1125954146	NA	3.60E-06	mr1280	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
vg1125954146	NA	3.57E-06	mr1729	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
vg1125954146	4.37E-09	4.37E-09	mr1191_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