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Detailed information for vg0629462477:

Variant ID: vg0629462477 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 29462477
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTCAAGAAAAAATTGGCAAATCTCTCTGGATTTTTCATCTTCCTCAGCAATGAAACACTACAACATTGCCAACACTGCAGCGTTACAGGCAAACTGATC[A/T]
GGTAGCTGCACCCATGAATATGCAGATGGATGACTACGAAGTTCATTATGAACAACACATCATTTGCTCAGAACAGCGCAGTGAGGAACAAATTTGACTG

Reverse complement sequence

CAGTCAAATTTGTTCCTCACTGCGCTGTTCTGAGCAAATGATGTGTTGTTCATAATGAACTTCGTAGTCATCCATCTGCATATTCATGGGTGCAGCTACC[T/A]
GATCAGTTTGCCTGTAACGCTGCAGTGTTGGCAATGTTGTAGTGTTTCATTGCTGAGGAAGATGAAAAATCCAGAGAGATTTGCCAATTTTTTCTTGAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.30%	2.70%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	91.60%	8.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	83.70%	16.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0629462477	A -> T	LOC_Os06g48700.1	3_prime_UTR_variant ; 266.0bp to feature; MODIFIER	silent_mutation	Average:49.55; most accessible tissue: Callus, score: 73.89	N	N	N	N
vg0629462477	A -> T	LOC_Os06g48690.1	upstream_gene_variant ; 1533.0bp to feature; MODIFIER	silent_mutation	Average:49.55; most accessible tissue: Callus, score: 73.89	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0629462477	1.66E-06	8.93E-06	mr1595_2	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