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Detailed information for vg0135957843:

Variant ID: vg0135957843 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 35957843
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, A: 0.17, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

CGTAAGCAAATGAGGATCAAGCTTAAAATATATGGATACAACTTTGGCAGACAATATCCATTTGCTAAGGGGCTGTTTGGTTTCCAGGGACTTATTCCAA[A/G]
TCCCTGTCACATCGGATGTTTGGACACTAATTTAGAGTATTAAACATACACTAATTACAAAACCCATTTCATAACATTGGACTAATTTGCGAGACGAATC

Reverse complement sequence

GATTCGTCTCGCAAATTAGTCCAATGTTATGAAATGGGTTTTGTAATTAGTGTATGTTTAATACTCTAAATTAGTGTCCAAACATCCGATGTGACAGGGA[T/C]
TTGGAATAAGTCCCTGGAAACCAAACAGCCCCTTAGCAAATGGATATTGTCTGCCAAAGTTGTATCCATATATTTTAAGCTTGATCCTCATTTGCTTACG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.10%	2.80%	0.25%	62.84%	NA
All Indica	2759	2.30%	0.70%	0.29%	96.77%	NA
All Japonica	1512	97.90%	0.00%	0.00%	2.05%	NA
Aus	269	0.70%	40.90%	0.00%	58.36%	NA
Indica I	595	1.20%	0.00%	0.67%	98.15%	NA
Indica II	465	1.90%	0.00%	0.00%	98.06%	NA
Indica III	913	1.30%	0.30%	0.00%	98.36%	NA
Indica Intermediate	786	4.50%	1.90%	0.51%	93.13%	NA
Temperate Japonica	767	98.80%	0.00%	0.00%	1.17%	NA
Tropical Japonica	504	97.20%	0.00%	0.00%	2.78%	NA
Japonica Intermediate	241	96.70%	0.00%	0.00%	3.32%	NA
VI/Aromatic	96	18.80%	0.00%	4.17%	77.08%	NA
Intermediate	90	53.30%	4.40%	0.00%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0135957843	A -> G	LOC_Os01g62110.1	upstream_gene_variant ; 4336.0bp to feature; MODIFIER	silent_mutation	Average:34.465; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N
vg0135957843	A -> G	LOC_Os01g62110-LOC_Os01g62120	intergenic_region ; MODIFIER	silent_mutation	Average:34.465; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N
vg0135957843	A -> DEL	N	N	silent_mutation	Average:34.465; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0135957843	4.08E-06	NA	mr1570	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
vg0135957843	NA	5.74E-09	mr1659	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
vg0135957843	NA	5.55E-15	mr1767_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