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Detailed information for vg0505143979:

Variant ID: vg0505143979 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5143979
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

AGTAAATTTCAGAATACAACATATGTAGAAACCAGGGACGGAGCTACCGTTGTTGCACCGGGGTCCTAGGACACCGATGGCCGGAGCTAAATTCCACTTG[A/G]
TACCTATGGTGTAGTTGAATGTGACCCCGGCAAAATTGTTGATTTAAACCCAGCCCATCTGATCATCTTGTATGAGCACAACTACTAATTAAATCTTGGG

Reverse complement sequence

CCCAAGATTTAATTAGTAGTTGTGCTCATACAAGATGATCAGATGGGCTGGGTTTAAATCAACAATTTTGCCGGGGTCACATTCAACTACACCATAGGTA[T/C]
CAAGTGGAATTTAGCTCCGGCCATCGGTGTCCTAGGACCCCGGTGCAACAACGGTAGCTCCGTCCCTGGTTTCTACATATGTTGTATTCTGAAATTTACT

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	81.60%	4.60%	2.86%	10.96%	NA
All Indica	2759	86.70%	7.80%	2.75%	2.72%	NA
All Japonica	1512	88.10%	0.10%	0.66%	11.18%	NA
Aus	269	15.60%	0.00%	15.61%	68.77%	NA
Indica I	595	92.30%	3.00%	2.86%	1.85%	NA
Indica II	465	85.80%	8.80%	4.73%	0.65%	NA
Indica III	913	88.80%	8.50%	0.88%	1.75%	NA
Indica Intermediate	786	80.70%	9.90%	3.69%	5.73%	NA
Temperate Japonica	767	85.30%	0.10%	0.52%	14.08%	NA
Tropical Japonica	504	89.70%	0.00%	0.99%	9.33%	NA
Japonica Intermediate	241	93.80%	0.00%	0.41%	5.81%	NA
VI/Aromatic	96	15.60%	0.00%	5.21%	79.17%	NA
Intermediate	90	82.20%	1.10%	2.22%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0505143979	A -> DEL	N	N	silent_mutation	Average:53.361; most accessible tissue: Callus, score: 69.21	N	N	N	N
vg0505143979	A -> G	LOC_Os05g09200.1	upstream_gene_variant ; 694.0bp to feature; MODIFIER	silent_mutation	Average:53.361; most accessible tissue: Callus, score: 69.21	N	N	N	N
vg0505143979	A -> G	LOC_Os05g09200-LOC_Os05g09210	intergenic_region ; MODIFIER	silent_mutation	Average:53.361; most accessible tissue: Callus, score: 69.21	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505143979	1.10E-06	3.35E-11	mr1352	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
vg0505143979	5.47E-06	4.83E-08	mr1352	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
vg0505143979	1.23E-06	1.23E-06	mr1905	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