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Detailed information for vg0400960642:

Variant ID: vg0400960642 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 960642
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGGTCAAAATTTGTTAAGTTTTCAAATAATTTTGGACAAAAAAGTTCTAAGTTATACAAAAATTTTGGAAATCCCGGCAACGTTCGTTTTAAGAAAAT[A/T]
TTGTGCCCCGGAAATTTTGAACCTAGAGTAAGTTAGTGTGTGTAAGAATATAATGATTTTCACATAATATTGCATCATATTATCTAGGCAGTTTATGTAG

Reverse complement sequence

CTACATAAACTGCCTAGATAATATGATGCAATATTATGTGAAAATCATTATATTCTTACACACACTAACTTACTCTAGGTTCAAAATTTCCGGGGCACAA[T/A]
ATTTTCTTAAAACGAACGTTGCCGGGATTTCCAAAATTTTTGTATAACTTAGAACTTTTTTGTCCAAAATTATTTGAAAACTTAACAAATTTTGACCAAT

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	94.80%	5.20%	0.06%	0.00%	NA
All Indica	2759	99.10%	0.80%	0.11%	0.00%	NA
All Japonica	1512	89.70%	10.30%	0.00%	0.00%	NA
Aus	269	98.10%	1.90%	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	98.00%	1.80%	0.22%	0.00%	NA
Indica Intermediate	786	99.20%	0.60%	0.13%	0.00%	NA
Temperate Japonica	767	88.00%	12.00%	0.00%	0.00%	NA
Tropical Japonica	504	97.60%	2.40%	0.00%	0.00%	NA
Japonica Intermediate	241	78.40%	21.60%	0.00%	0.00%	NA
VI/Aromatic	96	38.50%	61.50%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0400960642	A -> T	LOC_Os04g02560.1	upstream_gene_variant ; 601.0bp to feature; MODIFIER	silent_mutation	Average:21.975; most accessible tissue: Minghui63 root, score: 27.443	N	N	N	N
vg0400960642	A -> T	LOC_Os04g02560-LOC_Os04g02570	intergenic_region ; MODIFIER	silent_mutation	Average:21.975; most accessible tissue: Minghui63 root, score: 27.443	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400960642	1.02E-06	NA	mr1667_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