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Detailed information for vg0506206267:

Variant ID: vg0506206267 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6206267
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.58, C: 0.42, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

GTATACTTTTATGAAAGTATTTTTCAAGACAAATCTATTCATATAATTTTTACATTTTCAAACCCAATAACTTGAGAGTTATTCATGATTTATACTCCCT[T/C]
CGTTTCGAAATGTTTGACGCCGTTGACTTTTTAACACATGTTTGACCGTTCGTCTTATTCAAAAAATTTAAGTAATTATTAATTCTTTTCCTATTATTTG

Reverse complement sequence

CAAATAATAGGAAAAGAATTAATAATTACTTAAATTTTTTGAATAAGACGAACGGTCAAACATGTGTTAAAAAGTCAACGGCGTCAAACATTTCGAAACG[A/G]
AGGGAGTATAAATCATGAATAACTCTCAAGTTATTGGGTTTGAAAATGTAAAAATTATATGAATAGATTTGTCTTGAAAAATACTTTCATAAAAGTATAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.50%	27.70%	0.30%	20.52%	NA
All Indica	2759	60.30%	5.80%	0.11%	33.85%	NA
All Japonica	1512	40.60%	56.90%	0.66%	1.79%	NA
Aus	269	10.80%	89.20%	0.00%	0.00%	NA
Indica I	595	31.10%	2.70%	0.17%	66.05%	NA
Indica II	465	64.10%	5.80%	0.00%	30.11%	NA
Indica III	913	79.30%	4.80%	0.11%	15.77%	NA
Indica Intermediate	786	58.00%	9.20%	0.13%	32.70%	NA
Temperate Japonica	767	64.50%	33.20%	1.04%	1.17%	NA
Tropical Japonica	504	9.70%	87.90%	0.00%	2.38%	NA
Japonica Intermediate	241	29.00%	67.60%	0.83%	2.49%	NA
VI/Aromatic	96	82.30%	16.70%	0.00%	1.04%	NA
Intermediate	90	55.60%	34.40%	1.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0506206267	T -> DEL	N	N	silent_mutation	Average:17.771; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0506206267	T -> C	LOC_Os05g11070.1	upstream_gene_variant ; 348.0bp to feature; MODIFIER	silent_mutation	Average:17.771; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0506206267	T -> C	LOC_Os05g11064-LOC_Os05g11070	intergenic_region ; MODIFIER	silent_mutation	Average:17.771; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506206267	NA	5.87E-08	Grain_thickness	Ind_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
vg0506206267	6.89E-08	1.51E-16	Grain_width	Ind_All	YES	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
vg0506206267	NA	1.20E-06	mr1002	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
vg0506206267	NA	6.10E-06	mr1188	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
vg0506206267	NA	5.95E-08	mr1354	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
vg0506206267	NA	2.27E-06	mr1359_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
vg0506206267	NA	5.18E-06	mr1588_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