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Detailed information for vg0124403552:

Variant ID: vg0124403552 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24403552
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTATAGTTGCTCATTTCACTCGTCGACCTCATTCTTTTTAGCTACCACACAAAATTATCATCACGGATTATTTGCTTCAAGTCTCTTAAATTATTTTTTT[A/T]
AAAAAATTATTTTCGTATTGTGTTGCTTGAACCATTCGGAGCTAATATTTGTTAATTTCATATTTATAAATATTTAATTTATCATATGGAGCGTGACTAA

Reverse complement sequence

TTAGTCACGCTCCATATGATAAATTAAATATTTATAAATATGAAATTAACAAATATTAGCTCCGAATGGTTCAAGCAACACAATACGAAAATAATTTTTT[T/A]
AAAAAAATAATTTAAGAGACTTGAAGCAAATAATCCGTGATGATAATTTTGTGTGGTAGCTAAAAAGAATGAGGTCGACGAGTGAAATGAGCAACTATAA

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	79.90%	14.70%	5.08%	0.38%	NA
All Indica	2759	97.40%	1.50%	1.09%	0.04%	NA
All Japonica	1512	48.50%	37.00%	13.36%	1.12%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	98.70%	0.00%	1.34%	0.00%	NA
Indica II	465	98.10%	0.00%	1.94%	0.00%	NA
Indica III	913	96.10%	3.40%	0.55%	0.00%	NA
Indica Intermediate	786	97.50%	1.40%	1.02%	0.13%	NA
Temperate Japonica	767	47.70%	45.10%	7.17%	0.00%	NA
Tropical Japonica	504	43.80%	27.80%	25.40%	2.98%	NA
Japonica Intermediate	241	61.00%	30.30%	7.88%	0.83%	NA
VI/Aromatic	96	24.00%	75.00%	1.04%	0.00%	NA
Intermediate	90	73.30%	20.00%	6.67%	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
vg0124403552	A -> T	LOC_Os01g42880.1	upstream_gene_variant ; 2847.0bp to feature; MODIFIER	silent_mutation	Average:59.924; most accessible tissue: Callus, score: 91.301	N	N	N	N
vg0124403552	A -> T	LOC_Os01g42890.1	upstream_gene_variant ; 1512.0bp to feature; MODIFIER	silent_mutation	Average:59.924; most accessible tissue: Callus, score: 91.301	N	N	N	N
vg0124403552	A -> T	LOC_Os01g42900.1	downstream_gene_variant ; 4917.0bp to feature; MODIFIER	silent_mutation	Average:59.924; most accessible tissue: Callus, score: 91.301	N	N	N	N
vg0124403552	A -> T	LOC_Os01g42890-LOC_Os01g42900	intergenic_region ; MODIFIER	silent_mutation	Average:59.924; most accessible tissue: Callus, score: 91.301	N	N	N	N
vg0124403552	A -> DEL	N	N	silent_mutation	Average:59.924; most accessible tissue: Callus, score: 91.301	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124403552	2.70E-06	NA	mr1932	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