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Detailed information for vg0514727200:

Variant ID: vg0514727200 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14727200
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

GCTGCACCGACAGTTGTCGGCGGTGGCAGGTGGTGCCCCGTCGAATGGCGCGCGGCTCGCTGGATGGGATGGCTGTAGGAGTAGGAAACGGAGGGGAGGG[C/T]
GAAACTATTGAATGGGTTGGATTGGAAGGAGGGACTGTGAAGATGGTCGGCGACTAGCAGTGAAGAGGCTCGGTGGAGTGTGGTCATTATTTGGTTGCCG

Reverse complement sequence

CGGCAACCAAATAATGACCACACTCCACCGAGCCTCTTCACTGCTAGTCGCCGACCATCTTCACAGTCCCTCCTTCCAATCCAACCCATTCAATAGTTTC[G/A]
CCCTCCCCTCCGTTTCCTACTCCTACAGCCATCCCATCCAGCGAGCCGCGCGCCATTCGACGGGGCACCACCTGCCACCGCCGACAACTGTCGGTGCAGC

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	52.00%	47.70%	0.30%	0.02%	NA
All Indica	2759	79.70%	19.90%	0.36%	0.04%	NA
All Japonica	1512	7.90%	92.10%	0.00%	0.00%	NA
Aus	269	38.70%	61.30%	0.00%	0.00%	NA
Indica I	595	79.80%	19.70%	0.34%	0.17%	NA
Indica II	465	70.10%	29.50%	0.43%	0.00%	NA
Indica III	913	84.30%	15.70%	0.00%	0.00%	NA
Indica Intermediate	786	80.00%	19.20%	0.76%	0.00%	NA
Temperate Japonica	767	2.90%	97.10%	0.00%	0.00%	NA
Tropical Japonica	504	17.70%	82.30%	0.00%	0.00%	NA
Japonica Intermediate	241	3.30%	96.70%	0.00%	0.00%	NA
VI/Aromatic	96	0.00%	100.00%	0.00%	0.00%	NA
Intermediate	90	36.70%	58.90%	4.44%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0514727200	C -> T	LOC_Os05g25360.1	downstream_gene_variant ; 3724.0bp to feature; MODIFIER	silent_mutation	Average:80.405; most accessible tissue: Zhenshan97 young leaf, score: 89.772	N	N	N	N
vg0514727200	C -> T	LOC_Os05g25370.1	intron_variant ; MODIFIER	silent_mutation	Average:80.405; most accessible tissue: Zhenshan97 young leaf, score: 89.772	N	N	N	N
vg0514727200	C -> DEL	N	N	silent_mutation	Average:80.405; most accessible tissue: Zhenshan97 young leaf, score: 89.772	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514727200	2.44E-06	7.75E-08	mr1790	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