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Detailed information for vg1005431305:

Variant ID: vg1005431305 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5431305
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.04, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTAATATACATAGTATACATACATCCTATTTAACTGATATACTAGCTAATACCCTCTTTCCGATGCCCTCCTAGTAAGTCGAGAAACCACCCCTGACT[G/A]
CCGAGTTCCTTACGACAGCCCGTCATGACCATACAACCGGGGCTAAATACGGAGGAATACCCTCCCCAGGGAATTAACTTAGGATTATATATAGGCCCGG

Reverse complement sequence

CCGGGCCTATATATAATCCTAAGTTAATTCCCTGGGGAGGGTATTCCTCCGTATTTAGCCCCGGTTGTATGGTCATGACGGGCTGTCGTAAGGAACTCGG[C/T]
AGTCAGGGGTGGTTTCTCGACTTACTAGGAGGGCATCGGAAAGAGGGTATTAGCTAGTATATCAGTTAAATAGGATGTATGTATACTATGTATATTAGAA

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	54.90%	42.00%	2.86%	0.30%	NA
All Indica	2759	28.50%	69.30%	1.96%	0.22%	NA
All Japonica	1512	97.50%	1.50%	0.93%	0.07%	NA
Aus	269	74.30%	1.50%	21.93%	2.23%	NA
Indica I	595	7.90%	90.80%	1.34%	0.00%	NA
Indica II	465	19.10%	78.30%	2.15%	0.43%	NA
Indica III	913	47.80%	50.30%	1.64%	0.33%	NA
Indica Intermediate	786	27.40%	69.80%	2.67%	0.13%	NA
Temperate Japonica	767	98.30%	1.00%	0.65%	0.00%	NA
Tropical Japonica	504	98.00%	1.20%	0.60%	0.20%	NA
Japonica Intermediate	241	93.80%	3.70%	2.49%	0.00%	NA
VI/Aromatic	96	76.00%	18.80%	5.21%	0.00%	NA
Intermediate	90	65.60%	30.00%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1005431305	G -> A	LOC_Os10g10010.1	upstream_gene_variant ; 1649.0bp to feature; MODIFIER	silent_mutation	Average:42.732; most accessible tissue: Zhenshan97 root, score: 54.262	N	N	N	N
vg1005431305	G -> A	LOC_Os10g10020.1	upstream_gene_variant ; 4500.0bp to feature; MODIFIER	silent_mutation	Average:42.732; most accessible tissue: Zhenshan97 root, score: 54.262	N	N	N	N
vg1005431305	G -> A	LOC_Os10g10000.1	downstream_gene_variant ; 3558.0bp to feature; MODIFIER	silent_mutation	Average:42.732; most accessible tissue: Zhenshan97 root, score: 54.262	N	N	N	N
vg1005431305	G -> A	LOC_Os10g10010-LOC_Os10g10020	intergenic_region ; MODIFIER	silent_mutation	Average:42.732; most accessible tissue: Zhenshan97 root, score: 54.262	N	N	N	N
vg1005431305	G -> DEL	N	N	silent_mutation	Average:42.732; most accessible tissue: Zhenshan97 root, score: 54.262	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005431305	NA	3.74E-06	mr1114	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
vg1005431305	NA	1.12E-14	mr1199	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
vg1005431305	NA	1.14E-13	mr1147_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
vg1005431305	NA	9.05E-08	mr1212_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
vg1005431305	NA	3.95E-13	mr1649_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