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Detailed information for vg0700893465:

Variant ID: vg0700893465 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 893465
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAGTTTAGAGTCCATATAAAAATATAATTTAGAATTAAAAAAATCAAAATTAAAACTAAAACATATTGGGAGAAGAGTCTAGCATCCATATAAGAATAC[T/A]
ATTTATAAATAACTGAAATTCGAAATTAACAAATAAGGAATATTGGGAAAAAAATTCTAGCGACCATATAGGAATACAATTTAGAAATTACTGAAATTAA

Reverse complement sequence

TTAATTTCAGTAATTTCTAAATTGTATTCCTATATGGTCGCTAGAATTTTTTTCCCAATATTCCTTATTTGTTAATTTCGAATTTCAGTTATTTATAAAT[A/T]
GTATTCTTATATGGATGCTAGACTCTTCTCCCAATATGTTTTAGTTTTAATTTTGATTTTTTTAATTCTAAATTATATTTTTATATGGACTCTAAACTCT

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	62.80%	2.00%	4.25%	30.96%	NA
All Indica	2759	38.50%	3.40%	7.03%	51.07%	NA
All Japonica	1512	98.40%	0.00%	0.26%	1.32%	NA
Aus	269	92.60%	0.00%	0.74%	6.69%	NA
Indica I	595	19.20%	1.20%	4.54%	75.13%	NA
Indica II	465	81.10%	0.40%	1.51%	16.99%	NA
Indica III	913	24.60%	5.90%	12.92%	56.52%	NA
Indica Intermediate	786	44.10%	3.80%	5.34%	46.69%	NA
Temperate Japonica	767	98.60%	0.00%	0.39%	1.04%	NA
Tropical Japonica	504	97.60%	0.00%	0.20%	2.18%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	85.60%	0.00%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0700893465	T -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700893465	T -> A	LOC_Os07g02520.1	upstream_gene_variant ; 1849.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700893465	T -> A	LOC_Os07g02510-LOC_Os07g02520	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0700893465	NA	2.51E-06	mr1298	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