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Detailed information for vg0121402829:

Variant ID: vg0121402829 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21402829
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAAAATATGTTTTTTTTAAAAAAACTTAAGAGGTGATACGTTCACGTGGCAGCTTAGGAGCGGTCCGATGGATATTTAATTTTTATGACTATTTGGATG[A/T]
TATAAAAAGGGCCAGAATATAGACTAGATGGTTTTTTTTAATCAAAACATATATAACATACATAGTTCTTAAATTGTTCGTATAGTTGCTAGGAATAGAA

Reverse complement sequence

TTCTATTCCTAGCAACTATACGAACAATTTAAGAACTATGTATGTTATATATGTTTTGATTAAAAAAAACCATCTAGTCTATATTCTGGCCCTTTTTATA[T/A]
CATCCAAATAGTCATAAAAATTAAATATCCATCGGACCGCTCCTAAGCTGCCACGTGAACGTATCACCTCTTAAGTTTTTTTAAAAAAAACATATTTTTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.70%	35.90%	3.28%	11.15%	NA
All Indica	2759	77.90%	4.30%	5.40%	12.32%	NA
All Japonica	1512	1.30%	95.80%	0.07%	2.91%	NA
Aus	269	45.40%	3.70%	0.37%	50.56%	NA
Indica I	595	80.30%	2.70%	13.78%	3.19%	NA
Indica II	465	73.30%	7.10%	2.80%	16.77%	NA
Indica III	913	87.00%	1.90%	2.41%	8.76%	NA
Indica Intermediate	786	68.30%	6.90%	4.07%	20.74%	NA
Temperate Japonica	767	1.00%	95.70%	0.13%	3.13%	NA
Tropical Japonica	504	0.80%	97.60%	0.00%	1.59%	NA
Japonica Intermediate	241	2.90%	92.10%	0.00%	4.98%	NA
VI/Aromatic	96	28.10%	68.80%	3.12%	0.00%	NA
Intermediate	90	32.20%	58.90%	1.11%	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
vg0121402829	A -> T	LOC_Os01g38200.1	upstream_gene_variant ; 2339.0bp to feature; MODIFIER	silent_mutation	Average:22.201; most accessible tissue: Callus, score: 53.71	N	N	N	N
vg0121402829	A -> T	LOC_Os01g38200-LOC_Os01g38229	intergenic_region ; MODIFIER	silent_mutation	Average:22.201; most accessible tissue: Callus, score: 53.71	N	N	N	N
vg0121402829	A -> DEL	N	N	silent_mutation	Average:22.201; most accessible tissue: Callus, score: 53.71	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121402829	3.86E-06	NA	mr1603	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