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Detailed information for vg1109410629:

Variant ID: vg1109410629 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9410629
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

GATATCATCGATGAAGATCTGCCACAACACAAGGAGAAGGGAATTAAAATAGAATCAAAGGTGAACGTCGATCACGATGAGACGAAGAGCTCGTGTCCAT[G/A]
GATGCACGCTGACGCCGGTGAGACGATATCGCTCGAGATTATCCATTATTCGTCATGAACAATGGCACACACGGCCTCCCAGCTCTCCCGGTAGAGCTGC

Reverse complement sequence

GCAGCTCTACCGGGAGAGCTGGGAGGCCGTGTGTGCCATTGTTCATGACGAATAATGGATAATCTCGAGCGATATCGTCTCACCGGCGTCAGCGTGCATC[C/T]
ATGGACACGAGCTCTTCGTCTCATCGTGATCGACGTTCACCTTTGATTCTATTTTAATTCCCTTCTCCTTGTGTTGTGGCAGATCTTCATCGATGATATC

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	65.90%	33.00%	0.08%	0.99%	NA
All Indica	2759	44.20%	54.50%	0.11%	1.20%	NA
All Japonica	1512	97.30%	2.10%	0.00%	0.60%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	27.20%	69.90%	0.00%	2.86%	NA
Indica II	465	57.20%	41.30%	0.00%	1.51%	NA
Indica III	913	40.10%	59.50%	0.11%	0.33%	NA
Indica Intermediate	786	54.20%	44.80%	0.25%	0.76%	NA
Temperate Japonica	767	97.80%	2.20%	0.00%	0.00%	NA
Tropical Japonica	504	95.60%	2.60%	0.00%	1.79%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	71.10%	23.30%	1.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109410629	G -> A	LOC_Os11g16970.1	3_prime_UTR_variant ; 46.0bp to feature; MODIFIER	silent_mutation	Average:59.605; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N
vg1109410629	G -> A	LOC_Os11g16960.1	upstream_gene_variant ; 643.0bp to feature; MODIFIER	silent_mutation	Average:59.605; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N
vg1109410629	G -> A	LOC_Os11g16950.1	downstream_gene_variant ; 4252.0bp to feature; MODIFIER	silent_mutation	Average:59.605; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N
vg1109410629	G -> DEL	N	N	silent_mutation	Average:59.605; most accessible tissue: Zhenshan97 young leaf, score: 85.184	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109410629	NA	1.02E-06	mr1837	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
vg1109410629	NA	4.10E-07	mr1154_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