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Detailed information for vg0134535445:

Variant ID: vg0134535445 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 34535445
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.05, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTTTTAGTTAAAAATAGATTTGTTATTTATAAAAGCATGCATCAAATCATTAATCATTTACATATTTAGGCATGGGACATGCAATCAAGAGTCCACA[A/G]
CCATTCTGGTGAGATAGAAGTGAAGAAATTAATTATTAAGTAATAAAATAAAAATCTTAACTACCATACAGAAAAAAGGAAAGAGATGAGGAGAAGGGAT

Reverse complement sequence

ATCCCTTCTCCTCATCTCTTTCCTTTTTTCTGTATGGTAGTTAAGATTTTTATTTTATTACTTAATAATTAATTTCTTCACTTCTATCTCACCAGAATGG[T/C]
TGTGGACTCTTGATTGCATGTCCCATGCCTAAATATGTAAATGATTAATGATTTGATGCATGCTTTTATAAATAACAAATCTATTTTTAACTAAAAATTT

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	50.80%	17.50%	23.21%	8.40%	NA
All Indica	2759	66.10%	2.90%	30.77%	0.29%	NA
All Japonica	1512	32.90%	38.80%	8.80%	19.58%	NA
Aus	269	17.10%	50.60%	32.34%	0.00%	NA
Indica I	595	68.70%	3.50%	27.73%	0.00%	NA
Indica II	465	78.90%	0.40%	20.43%	0.22%	NA
Indica III	913	62.90%	0.80%	36.04%	0.33%	NA
Indica Intermediate	786	60.20%	6.20%	33.08%	0.51%	NA
Temperate Japonica	767	44.70%	45.80%	5.22%	4.30%	NA
Tropical Japonica	504	16.10%	40.30%	5.56%	38.10%	NA
Japonica Intermediate	241	30.30%	13.30%	26.97%	29.46%	NA
VI/Aromatic	96	4.20%	4.20%	9.38%	82.29%	NA
Intermediate	90	36.70%	26.70%	21.11%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0134535445	A -> G	LOC_Os01g59700.1	upstream_gene_variant ; 1428.0bp to feature; MODIFIER	silent_mutation	Average:24.894; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0134535445	A -> G	LOC_Os01g59690.1	downstream_gene_variant ; 1674.0bp to feature; MODIFIER	silent_mutation	Average:24.894; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0134535445	A -> G	LOC_Os01g59690-LOC_Os01g59700	intergenic_region ; MODIFIER	silent_mutation	Average:24.894; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N
vg0134535445	A -> DEL	N	N	silent_mutation	Average:24.894; most accessible tissue: Zhenshan97 root, score: 51.776	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0134535445	9.28E-06	NA	mr1510	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