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Detailed information for vg0142045683:

Variant ID: vg0142045683 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 42045683
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

GTACTTGCTCTAAGGCGGCTCAGCGAAGATGAGGTCCTGTGGCAACAATGGTGGGACAACCAGTGGCGGATCCAGAAAATCGATTCGTTGGTGTCATAAC[G/A]
TGTCTATCGGTGTCATAGTATGCTAATTATGTTTAGATCATAGTGTTATAACATATGGATAAACAGTTTTGCTATAGGTTTTGCCGAAAGTCGTCGGTGT

Reverse complement sequence

ACACCGACGACTTTCGGCAAAACCTATAGCAAAACTGTTTATCCATATGTTATAACACTATGATCTAAACATAATTAGCATACTATGACACCGATAGACA[C/T]
GTTATGACACCAACGAATCGATTTTCTGGATCCGCCACTGGTTGTCCCACCATTGTTGCCACAGGACCTCATCTTCGCTGAGCCGCCTTAGAGCAAGTAC

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	93.00%	7.00%	0.02%	0.00%	NA
All Indica	2759	88.40%	11.60%	0.00%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	87.20%	12.80%	0.00%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	80.50%	19.50%	0.00%	0.00%	NA
Indica Intermediate	786	92.70%	7.30%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	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
vg0142045683	G -> A	LOC_Os01g72500.1	downstream_gene_variant ; 2770.0bp to feature; MODIFIER	silent_mutation	Average:46.072; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0142045683	G -> A	LOC_Os01g72500-LOC_Os01g72510	intergenic_region ; MODIFIER	silent_mutation	Average:46.072; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0142045683	5.00E-06	NA	mr1336	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
vg0142045683	4.58E-07	3.81E-10	mr1336	Ind_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