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Detailed information for vg0136326230:

Variant ID: vg0136326230 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 36326230
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: 0.04, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTAGGTTTGATAAGGGACAGACATACATATTTGCTCTAAGTACAGAATATAGTGCTAGCCTCTGAAGTAGGCGGTGTTGTCCCATGCTGATCATCACG[G/A]
CTATCAGTTGTGGCCTATGCATAAGCAATATTAATATAAGAATTTACAATTGTTTATATGCAAGAGAGTACACATTGCTGCAGAATGAAGCTATTAGATT

Reverse complement sequence

AATCTAATAGCTTCATTCTGCAGCAATGTGTACTCTCTTGCATATAAACAATTGTAAATTCTTATATTAATATTGCTTATGCATAGGCCACAACTGATAG[C/T]
CGTGATGATCAGCATGGGACAACACCGCCTACTTCAGAGGCTAGCACTATATTCTGTACTTAGAGCAAATATGTATGTCTGTCCCTTATCAAACCTAACT

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	82.20%	15.70%	0.44%	1.67%	NA
All Indica	2759	75.20%	24.50%	0.22%	0.11%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	46.50%	19.70%	5.58%	28.25%	NA
Indica I	595	88.70%	11.30%	0.00%	0.00%	NA
Indica II	465	95.30%	4.70%	0.00%	0.00%	NA
Indica III	913	60.70%	39.30%	0.00%	0.00%	NA
Indica Intermediate	786	69.80%	29.00%	0.76%	0.38%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0136326230	G -> A	LOC_Os01g62740.1	downstream_gene_variant ; 1214.0bp to feature; MODIFIER	silent_mutation	Average:42.136; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0136326230	G -> A	LOC_Os01g62750.1	intron_variant ; MODIFIER	silent_mutation	Average:42.136; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0136326230	G -> DEL	N	N	silent_mutation	Average:42.136; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0136326230	NA	2.18E-07	mr1133	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
vg0136326230	NA	1.04E-06	mr1192	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
vg0136326230	NA	3.72E-07	mr1213	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
vg0136326230	NA	6.39E-06	mr1727	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
vg0136326230	NA	1.27E-09	mr1887	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
vg0136326230	NA	1.26E-09	mr1887	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
vg0136326230	NA	1.48E-06	mr1133_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