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Detailed information for vg0901413043:

Variant ID: vg0901413043 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1413043
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, G: 0.12, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

CACCCCTGACTGCCGAGTTCCTTACGACAGCCCGTCATGACCATCCAACCGGGGCTAAATACGGAGGAATACCCTCCCCAGGAAATTAACTTAGGATTAT[A/G]
TATAGGCGCGGAGGAATACTCGTAGTGAGCTGTCACCATCAGCGGCTCACCTCTTATCCGCAATATGTAACCCCAAATAATGATATCCCGTACTCTAGAC

Reverse complement sequence

GTCTAGAGTACGGGATATCATTATTTGGGGTTACATATTGCGGATAAGAGGTGAGCCGCTGATGGTGACAGCTCACTACGAGTATTCCTCCGCGCCTATA[T/C]
ATAATCCTAAGTTAATTTCCTGGGGAGGGTATTCCTCCGTATTTAGCCCCGGTTGGATGGTCATGACGGGCTGTCGTAAGGAACTCGGCAGTCAGGGGTG

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	61.90%	26.20%	0.11%	11.81%	NA
All Indica	2759	93.30%	5.50%	0.07%	1.12%	NA
All Japonica	1512	1.80%	66.70%	0.13%	31.42%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	93.10%	6.40%	0.00%	0.50%	NA
Indica II	465	91.60%	8.20%	0.00%	0.22%	NA
Indica III	913	96.70%	1.80%	0.22%	1.31%	NA
Indica Intermediate	786	90.50%	7.60%	0.00%	1.91%	NA
Temperate Japonica	767	0.90%	97.40%	0.00%	1.69%	NA
Tropical Japonica	504	2.60%	25.80%	0.20%	71.43%	NA
Japonica Intermediate	241	2.90%	54.40%	0.41%	42.32%	NA
VI/Aromatic	96	11.50%	52.10%	0.00%	36.46%	NA
Intermediate	90	50.00%	31.10%	1.11%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0901413043	A -> G	LOC_Os09g03000.1	upstream_gene_variant ; 2549.0bp to feature; MODIFIER	silent_mutation	Average:34.647; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N
vg0901413043	A -> G	LOC_Os09g03010.1	downstream_gene_variant ; 1951.0bp to feature; MODIFIER	silent_mutation	Average:34.647; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N
vg0901413043	A -> G	LOC_Os09g03000-LOC_Os09g03010	intergenic_region ; MODIFIER	silent_mutation	Average:34.647; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N
vg0901413043	A -> DEL	N	N	silent_mutation	Average:34.647; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901413043	NA	4.22E-07	mr1042_2	Jap_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
vg0901413043	1.02E-06	1.02E-06	mr1335_2	Jap_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
vg0901413043	NA	3.84E-06	mr1544_2	Jap_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
vg0901413043	2.24E-06	1.70E-08	mr1680_2	Jap_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