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Detailed information for vg0116741597:

Variant ID: vg0116741597 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 16741597
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.56, G: 0.44, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GCCTAAAGCCACGAACCAAACTCATACTAAGAGTCCTAAACACCTTAGAAAACCTTCTAGTACAAGACACAAACTTAACATAACCAATCGTACCAAATTT[A/G]
GACTCCTTCCAAATTCGACTCCGCATCCCATACGCACACAATACCTCCATCGTATGCCATATGGAATCTTCACCAACCATGTGCATCAACTCTAGCCTTA

Reverse complement sequence

TAAGGCTAGAGTTGATGCACATGGTTGGTGAAGATTCCATATGGCATACGATGGAGGTATTGTGTGCGTATGGGATGCGGAGTCGAATTTGGAAGGAGTC[T/C]
AAATTTGGTACGATTGGTTATGTTAAGTTTGTGTCTTGTACTAGAAGGTTTTCTAAGGTGTTTAGGACTCTTAGTATGAGTTTGGTTCGTGGCTTTAGGC

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	61.60%	37.90%	0.44%	0.06%	NA
All Indica	2759	95.90%	3.30%	0.69%	0.11%	NA
All Japonica	1512	2.60%	97.40%	0.00%	0.00%	NA
Aus	269	68.00%	31.60%	0.37%	0.00%	NA
Indica I	595	96.50%	2.40%	1.01%	0.17%	NA
Indica II	465	94.80%	4.90%	0.22%	0.00%	NA
Indica III	913	98.60%	0.80%	0.55%	0.11%	NA
Indica Intermediate	786	93.00%	6.00%	0.89%	0.13%	NA
Temperate Japonica	767	0.90%	99.10%	0.00%	0.00%	NA
Tropical Japonica	504	5.60%	94.40%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	6.20%	93.80%	0.00%	0.00%	NA
Intermediate	90	42.20%	56.70%	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
vg0116741597	A -> G	LOC_Os01g29880.1	upstream_gene_variant ; 683.0bp to feature; MODIFIER	silent_mutation	Average:25.211; most accessible tissue: Zhenshan97 flag leaf, score: 43.728	N	N	N	N
vg0116741597	A -> G	LOC_Os01g29890.1	downstream_gene_variant ; 1584.0bp to feature; MODIFIER	silent_mutation	Average:25.211; most accessible tissue: Zhenshan97 flag leaf, score: 43.728	N	N	N	N
vg0116741597	A -> G	LOC_Os01g29880-LOC_Os01g29890	intergenic_region ; MODIFIER	silent_mutation	Average:25.211; most accessible tissue: Zhenshan97 flag leaf, score: 43.728	N	N	N	N
vg0116741597	A -> DEL	N	N	silent_mutation	Average:25.211; most accessible tissue: Zhenshan97 flag leaf, score: 43.728	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0116741597	1.39E-07	NA	mr1707_2	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
vg0116741597	1.10E-06	NA	mr1707_2	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
vg0116741597	NA	3.64E-13	mr1770_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