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Detailed information for vg0515273812:

Variant ID: vg0515273812 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 15273812
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: 90. )

Flanking Sequence (100 bp) in Reference Genome:

CGTCGTCGGTCGTCGTTTGTCGTAGTTCTTTGCTTCGTTGAGTTCGCATCGTCGTCCTCTTCATGTTGGTGTCTTCGGAAAGCACAACCGAGCTCTTTAG[C/T]
ACTGGTAACCTCGTGGTCCTGTGCCATGGCCGGCGATGATGTCGTGATGACATCATAATTTCCTTTTTATTAGTTTTTCTGTATTAGATGAAAATCGATT

Reverse complement sequence

AATCGATTTTCATCTAATACAGAAAAACTAATAAAAAGGAAATTATGATGTCATCACGACATCATCGCCGGCCATGGCACAGGACCACGAGGTTACCAGT[G/A]
CTAAAGAGCTCGGTTGTGCTTTCCGAAGACACCAACATGAAGAGGACGACGATGCGAACTCAACGAAGCAAAGAACTACGACAAACGACGACCGACGACG

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	51.70%	42.00%	1.18%	5.12%	NA
All Indica	2759	37.80%	56.70%	0.47%	5.00%	NA
All Japonica	1512	74.10%	22.20%	2.18%	1.46%	NA
Aus	269	52.00%	19.70%	1.86%	26.39%	NA
Indica I	595	22.00%	76.30%	0.34%	1.34%	NA
Indica II	465	60.00%	39.40%	0.22%	0.43%	NA
Indica III	913	43.20%	46.10%	0.22%	10.51%	NA
Indica Intermediate	786	30.50%	64.40%	1.02%	4.07%	NA
Temperate Japonica	767	92.30%	6.10%	1.43%	0.13%	NA
Tropical Japonica	504	46.80%	48.20%	2.78%	2.18%	NA
Japonica Intermediate	241	73.40%	19.10%	3.32%	4.15%	NA
VI/Aromatic	96	92.70%	1.00%	2.08%	4.17%	NA
Intermediate	90	55.60%	33.30%	3.33%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0515273812	C -> T	LOC_Os05g26260.1	downstream_gene_variant ; 3681.0bp to feature; MODIFIER	silent_mutation	Average:61.923; most accessible tissue: Callus, score: 86.635	N	N	N	N
vg0515273812	C -> T	LOC_Os05g26250.1	intron_variant ; MODIFIER	silent_mutation	Average:61.923; most accessible tissue: Callus, score: 86.635	N	N	N	N
vg0515273812	C -> T	LOC_Os05g26359.1	intron_variant ; MODIFIER	silent_mutation	Average:61.923; most accessible tissue: Callus, score: 86.635	N	N	N	N
vg0515273812	C -> T	LOC_Os05g26400.1	intron_variant ; MODIFIER	silent_mutation	Average:61.923; most accessible tissue: Callus, score: 86.635	N	N	N	N
vg0515273812	C -> DEL	N	N	silent_mutation	Average:61.923; most accessible tissue: Callus, score: 86.635	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0515273812	NA	6.41E-07	mr1749	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