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Detailed information for vg0514534416:

Variant ID: vg0514534416 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14534416
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGTGCAAAGGATAACAAAGGATGGCATAGTAAAGCTCATTTGCATAAACAGAATTTAGTAAACATTTTAAAGAATAATAAATCAATTGAATAATTAAT[C/T]
AGTATTAAATAAACACCATACAACACACCTATCTTGCATAGGCCCAACCTCATTTGAACAACCAACCCCGGTTGTACAAATCAAACCTCCATACCAGGAA

Reverse complement sequence

TTCCTGGTATGGAGGTTTGATTTGTACAACCGGGGTTGGTTGTTCAAATGAGGTTGGGCCTATGCAAGATAGGTGTGTTGTATGGTGTTTATTTAATACT[G/A]
ATTAATTATTCAATTGATTTATTATTCTTTAAAATGTTTACTAAATTCTGTTTATGCAAATGAGCTTTACTATGCCATCCTTTGTTATCCTTTGCACTTG

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	93.00%	4.90%	2.14%	0.00%	NA
All Indica	2759	88.30%	8.20%	3.52%	0.00%	NA
All Japonica	1512	99.50%	0.30%	0.26%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.10%	1.00%	3.87%	0.00%	NA
Indica II	465	69.20%	20.90%	9.89%	0.00%	NA
Indica III	913	88.50%	11.00%	0.55%	0.00%	NA
Indica Intermediate	786	94.30%	2.80%	2.93%	0.00%	NA
Temperate Japonica	767	99.10%	0.50%	0.39%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	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
vg0514534416	C -> T	LOC_Os05g25100.1	downstream_gene_variant ; 910.0bp to feature; MODIFIER	silent_mutation	Average:32.697; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0514534416	C -> T	LOC_Os05g25090-LOC_Os05g25100	intergenic_region ; MODIFIER	silent_mutation	Average:32.697; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514534416	1.73E-10	1.38E-35	mr1039	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
vg0514534416	8.96E-09	1.49E-20	mr1039	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
vg0514534416	6.36E-06	NA	mr1632	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
vg0514534416	NA	4.73E-09	mr1632	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
vg0514534416	1.05E-13	7.07E-39	mr1039_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
vg0514534416	8.42E-11	6.72E-22	mr1039_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
vg0514534416	6.79E-06	NA	mr1514_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
vg0514534416	1.83E-14	NA	mr1632_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
vg0514534416	4.39E-12	3.13E-18	mr1632_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