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Detailed information for vg0507049696:

Variant ID: vg0507049696 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7049696
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

AGTACCATTCGCTTCTGCCTAGTATATTAGTAAGAAATATTTAAATCTTCCAGCTTGTATGATAGACAAACAAATACACACGGGCTTACATTGTTCGTGC[T/C]
TAGTTTTTTTAGAGGAGATGTATCGATCAGTAAGCACTAAGAGCACCCGCAATGGTAAAGTAAGTTGCTCTCTATAACATATGTACATCTCAGCAATAGA

Reverse complement sequence

TCTATTGCTGAGATGTACATATGTTATAGAGAGCAACTTACTTTACCATTGCGGGTGCTCTTAGTGCTTACTGATCGATACATCTCCTCTAAAAAAACTA[A/G]
GCACGAACAATGTAAGCCCGTGTGTATTTGTTTGTCTATCATACAAGCTGGAAGATTTAAATATTTCTTACTAATATACTAGGCAGAAGCGAATGGTACT

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	85.50%	13.20%	1.25%	0.00%	NA
All Indica	2759	75.80%	22.20%	2.03%	0.00%	NA
All Japonica	1512	99.80%	0.10%	0.07%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	89.40%	6.20%	4.37%	0.00%	NA
Indica II	465	79.60%	18.30%	2.15%	0.00%	NA
Indica III	913	71.90%	27.60%	0.55%	0.00%	NA
Indica Intermediate	786	67.70%	30.40%	1.91%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	12.20%	1.11%	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
vg0507049696	T -> C	LOC_Os05g12280.1	downstream_gene_variant ; 185.0bp to feature; MODIFIER	silent_mutation	Average:60.8; most accessible tissue: Minghui63 flag leaf, score: 81.312	N	N	N	N
vg0507049696	T -> C	LOC_Os05g12270-LOC_Os05g12280	intergenic_region ; MODIFIER	silent_mutation	Average:60.8; most accessible tissue: Minghui63 flag leaf, score: 81.312	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507049696	9.14E-08	2.51E-08	mr1593	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
vg0507049696	4.10E-07	3.66E-07	mr1593	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
vg0507049696	1.35E-06	NA	mr1593_2	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
vg0507049696	4.92E-06	1.30E-07	mr1593_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