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Detailed information for vg0514549761:

Variant ID: vg0514549761 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14549761
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GGCAAGTAATACTTGCTGCCTAAAACACGGTCTCCAGGCAAATATATTCTGGTGAATATACCGCAGCCGATGTTTAGGACTCCACTACCTTGTGCTCAAC[C/T]
AAATTTCAAATAATCTCATTTTTCAAAACATATTCTCGGAAAGTAACACATGTGGGTAATCATCGTGAGATGTTGACCTCTGTGAGATGGGCGAGATGCT

Reverse complement sequence

AGCATCTCGCCCATCTCACAGAGGTCAACATCTCACGATGATTACCCACATGTGTTACTTTCCGAGAATATGTTTTGAAAAATGAGATTATTTGAAATTT[G/A]
GTTGAGCACAAGGTAGTGGAGTCCTAAACATCGGCTGCGGTATATTCACCAGAATATATTTGCCTGGAGACCGTGTTTTAGGCAGCAAGTATTACTTGCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.10%	14.40%	15.23%	22.28%	NA
All Indica	2759	21.40%	19.60%	23.05%	35.92%	NA
All Japonica	1512	98.10%	0.10%	0.26%	1.59%	NA
Aus	269	19.70%	48.70%	25.28%	6.32%	NA
Indica I	595	33.30%	2.70%	16.47%	47.56%	NA
Indica II	465	12.50%	32.70%	21.29%	33.55%	NA
Indica III	913	19.10%	24.30%	29.13%	27.49%	NA
Indica Intermediate	786	20.50%	19.20%	22.01%	38.30%	NA
Temperate Japonica	767	97.40%	0.10%	0.39%	2.09%	NA
Tropical Japonica	504	99.00%	0.00%	0.20%	0.79%	NA
Japonica Intermediate	241	98.30%	0.00%	0.00%	1.66%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	56.70%	6.70%	13.33%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0514549761	C -> T	LOC_Os05g25110.1	upstream_gene_variant ; 892.0bp to feature; MODIFIER	silent_mutation	Average:13.166; most accessible tissue: Callus, score: 39.388	N	N	N	N
vg0514549761	C -> T	LOC_Os05g25120.1	downstream_gene_variant ; 4663.0bp to feature; MODIFIER	silent_mutation	Average:13.166; most accessible tissue: Callus, score: 39.388	N	N	N	N
vg0514549761	C -> T	LOC_Os05g25110-LOC_Os05g25120	intergenic_region ; MODIFIER	silent_mutation	Average:13.166; most accessible tissue: Callus, score: 39.388	N	N	N	N
vg0514549761	C -> DEL	N	N	silent_mutation	Average:13.166; most accessible tissue: Callus, score: 39.388	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514549761	NA	1.66E-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
vg0514549761	9.56E-06	NA	Grain_width	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
vg0514549761	8.07E-10	4.41E-19	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