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Detailed information for vg0506795354:

Variant ID: vg0506795354 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6795354
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.79, G: 0.21, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:

TCCATGTAAAAATGCTGTCTTCACATCTAACTGCTCAAGCTCAAGATCATGCATAGCAACAATACTGAAGAATGTGCGAATTGAACTATGCTTTACAACT[A/G]
GAGAGAACACATCATTATAATCAACACCAGCAATTTGACTAAAACCTTTTGCTACTAAACTTGCCTTAAACCTCGGAGGGTCGCTAGGAGATAAACCCTC

Reverse complement sequence

GAGGGTTTATCTCCTAGCGACCCTCCGAGGTTTAAGGCAAGTTTAGTAGCAAAAGGTTTTAGTCAAATTGCTGGTGTTGATTATAATGATGTGTTCTCTC[T/C]
AGTTGTAAAGCATAGTTCAATTCGCACATTCTTCAGTATTGTTGCTATGCATGATCTTGAGCTTGAGCAGTTAGATGTGAAGACAGCATTTTTACATGGA

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	81.90%	1.90%	14.41%	1.82%	NA
All Indica	2759	96.30%	0.60%	2.90%	0.18%	NA
All Japonica	1512	59.30%	4.00%	32.21%	4.56%	NA
Aus	269	84.40%	1.90%	11.52%	2.23%	NA
Indica I	595	99.30%	0.00%	0.67%	0.00%	NA
Indica II	465	96.60%	1.30%	1.94%	0.22%	NA
Indica III	913	94.40%	0.40%	5.04%	0.11%	NA
Indica Intermediate	786	96.20%	0.80%	2.67%	0.38%	NA
Temperate Japonica	767	88.70%	0.50%	9.39%	1.43%	NA
Tropical Japonica	504	24.60%	9.30%	58.13%	7.94%	NA
Japonica Intermediate	241	38.20%	3.70%	50.62%	7.47%	NA
VI/Aromatic	96	20.80%	5.20%	70.83%	3.12%	NA
Intermediate	90	76.70%	3.30%	16.67%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0506795354	A -> DEL	N	N	silent_mutation	Average:22.6; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0506795354	A -> G	LOC_Os05g11940.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:22.6; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0506795354	A -> G	LOC_Os05g11920.1	upstream_gene_variant ; 2575.0bp to feature; MODIFIER	silent_mutation	Average:22.6; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0506795354	A -> G	LOC_Os05g11910.1	downstream_gene_variant ; 3763.0bp to feature; MODIFIER	silent_mutation	Average:22.6; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0506795354	A -> G	LOC_Os05g11930.1	downstream_gene_variant ; 1624.0bp to feature; MODIFIER	silent_mutation	Average:22.6; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506795354	3.13E-06	NA	Grain_thickness	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0506795354	2.85E-06	7.27E-13	mr1593	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
vg0506795354	7.65E-06	6.32E-17	mr1593	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
vg0506795354	9.46E-07	2.08E-15	mr1593_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
vg0506795354	5.29E-07	NA	mr1593_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