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Detailed information for vg0135984043:

Variant ID: vg0135984043 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 35984043
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:

AATGTCCTTTGAACATTTGCCACGGGTTAGTGGTAGGTGCAGCTTAACTGGCGATCATTGTCATCCTAAGAAGGTTGTGGTCGGCACACTTGTTACTCTT[G/A]
TGGTTTCATGTCGATCTTGGCTGTAATCGAGCACAGTAACCATGTAGCAACATGTTTCTGCTCAAAGACGAGCCAGTTTCCAAATTGTCTTCAGTATACA

Reverse complement sequence

TGTATACTGAAGACAATTTGGAAACTGGCTCGTCTTTGAGCAGAAACATGTTGCTACATGGTTACTGTGCTCGATTACAGCCAAGATCGACATGAAACCA[C/T]
AAGAGTAACAAGTGTGCCGACCACAACCTTCTTAGGATGACAATGATCGCCAGTTAAGCTGCACCTACCACTAACCCGTGGCAAATGTTCAAAGGACATT

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	97.90%	2.10%	0.00%	0.00%	NA
All Indica	2759	96.60%	3.40%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.90%	9.10%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	98.00%	2.00%	0.00%	0.00%	NA
Indica Intermediate	786	97.10%	2.90%	0.00%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0135984043	G -> A	LOC_Os01g62160.1	3_prime_UTR_variant ; 344.0bp to feature; MODIFIER	silent_mutation	Average:74.26; most accessible tissue: Zhenshan97 flower, score: 85.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0135984043	NA	9.95E-08	mr1458_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