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Detailed information for vg0502043743:

Variant ID: vg0502043743 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 2043743
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

GCTTTGGCAATTTATGCTCGCAATGGTGTGGCCCAATGCTGATAAAATCCTTTTTAATGCGGTTATATAATTCTTTGGAATTATTGCAATGCAAATTGAA[A/G]
GGTACCCGACAGAAAAGTGTTATACTATTTTTGTAAGCTTTTTTAGGCTGCAAAAGCTGTCTGGGTTGATTTAAGATGACTTGTTTTTACAATGGTCATT

Reverse complement sequence

AATGACCATTGTAAAAACAAGTCATCTTAAATCAACCCAGACAGCTTTTGCAGCCTAAAAAAGCTTACAAAAATAGTATAACACTTTTCTGTCGGGTACC[T/C]
TTCAATTTGCATTGCAATAATTCCAAAGAATTATATAACCGCATTAAAAAGGATTTTATCAGCATTGGGCCACACCATTGCGAGCATAAATTGCCAAAGC

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	76.10%	8.10%	1.95%	13.84%	NA
All Indica	2759	69.20%	10.70%	2.54%	17.54%	NA
All Japonica	1512	91.10%	0.30%	0.40%	8.13%	NA
Aus	269	62.10%	19.00%	3.72%	15.24%	NA
Indica I	595	82.00%	6.40%	2.35%	9.24%	NA
Indica II	465	78.70%	1.90%	2.15%	17.20%	NA
Indica III	913	55.60%	17.70%	2.30%	24.32%	NA
Indica Intermediate	786	69.70%	10.90%	3.18%	16.16%	NA
Temperate Japonica	767	97.80%	0.10%	0.13%	1.96%	NA
Tropical Japonica	504	81.90%	0.40%	0.60%	17.06%	NA
Japonica Intermediate	241	89.20%	0.80%	0.83%	9.13%	NA
VI/Aromatic	96	65.60%	29.20%	5.21%	0.00%	NA
Intermediate	90	87.80%	4.40%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0502043743	A -> DEL	N	N	silent_mutation	Average:33.235; most accessible tissue: Zhenshan97 flag leaf, score: 74.162	N	N	N	N
vg0502043743	A -> G	LOC_Os05g04430.1	upstream_gene_variant ; 433.0bp to feature; MODIFIER	silent_mutation	Average:33.235; most accessible tissue: Zhenshan97 flag leaf, score: 74.162	N	N	N	N
vg0502043743	A -> G	LOC_Os05g04440.1	upstream_gene_variant ; 1252.0bp to feature; MODIFIER	silent_mutation	Average:33.235; most accessible tissue: Zhenshan97 flag leaf, score: 74.162	N	N	N	N
vg0502043743	A -> G	LOC_Os05g04430-LOC_Os05g04440	intergenic_region ; MODIFIER	silent_mutation	Average:33.235; most accessible tissue: Zhenshan97 flag leaf, score: 74.162	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0502043743	NA	1.48E-06	mr1798	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
vg0502043743	2.46E-07	7.81E-07	mr1946	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