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Detailed information for vg0504907926:

Variant ID: vg0504907926 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 4907926
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCATAACGGGCAGAATCTGGGCTGTGGCTATAAATAGCCCCCTCCCCTCACTTGTGAGGGCTGCTGGTTCCATTCCAATCATTTGTGCCCTTGGCTTG[T/C]
TCTCTCTCTAGCACTTTTGAGCCTTGCTTTCTTGTTTCCCCTCTCACCTGTGTTCGATTTGGATTTGGTGTGTGTGTGTGAGAGTTGTGGATTCGAGTTT

Reverse complement sequence

AAACTCGAATCCACAACTCTCACACACACACACCAAATCCAAATCGAACACAGGTGAGAGGGGAAACAAGAAAGCAAGGCTCAAAAGTGCTAGAGAGAGA[A/G]
CAAGCCAAGGGCACAAATGATTGGAATGGAACCAGCAGCCCTCACAAGTGAGGGGAGGGGGCTATTTATAGCCACAGCCCAGATTCTGCCCGTTATGCAC

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	71.20%	2.00%	8.32%	18.51%	NA
All Indica	2759	64.00%	0.30%	11.45%	24.25%	NA
All Japonica	1512	93.10%	5.60%	0.86%	0.46%	NA
Aus	269	8.90%	0.00%	21.19%	69.89%	NA
Indica I	595	90.90%	0.00%	3.53%	5.55%	NA
Indica II	465	34.60%	0.20%	14.84%	50.32%	NA
Indica III	913	62.00%	0.30%	14.68%	23.00%	NA
Indica Intermediate	786	63.40%	0.50%	11.70%	24.43%	NA
Temperate Japonica	767	97.30%	2.50%	0.00%	0.26%	NA
Tropical Japonica	504	88.30%	11.10%	0.20%	0.40%	NA
Japonica Intermediate	241	89.60%	4.10%	4.98%	1.24%	NA
VI/Aromatic	96	91.70%	0.00%	3.12%	5.21%	NA
Intermediate	90	86.70%	2.20%	4.44%	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
vg0504907926	T -> DEL	N	N	silent_mutation	Average:20.951; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N
vg0504907926	T -> C	LOC_Os05g08870.1	upstream_gene_variant ; 4846.0bp to feature; MODIFIER	silent_mutation	Average:20.951; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N
vg0504907926	T -> C	LOC_Os05g08880.1	intron_variant ; MODIFIER	silent_mutation	Average:20.951; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0504907926	NA	4.75E-13	Grain_width	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
vg0504907926	NA	9.55E-06	mr1113_2	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
vg0504907926	4.69E-06	NA	mr1718_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