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Detailed information for vg0703531849:

Variant ID: vg0703531849 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 3531849
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGTACTAGAAAATAAGCGTGCCTTTTGGCACACTGAATGGATAACCCGTAGATATTGTATATTTTGGGTGCATAAGTATTGTATAGGTTATTTAAAAA[A/T]
TAGTTCATATATGAAATGGAAAAAAGATGGATCAAGCAGCGGTCGTCGATCATGTTTTAAAATCTAGGACCCGACAAATCTATATGTGAAAGGCCCTTCA

Reverse complement sequence

TGAAGGGCCTTTCACATATAGATTTGTCGGGTCCTAGATTTTAAAACATGATCGACGACCGCTGCTTGATCCATCTTTTTTCCATTTCATATATGAACTA[T/A]
TTTTTAAATAACCTATACAATACTTATGCACCCAAAATATACAATATCTACGGGTTATCCATTCAGTGTGCCAAAAGGCACGCTTATTTTCTAGTACTTC

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	86.70%	11.50%	1.82%	0.00%	NA
All Indica	2759	95.20%	3.30%	1.45%	0.00%	NA
All Japonica	1512	67.60%	29.40%	3.04%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	82.50%	11.80%	5.71%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	96.90%	2.30%	0.76%	0.00%	NA
Temperate Japonica	767	48.90%	46.70%	4.43%	0.00%	NA
Tropical Japonica	504	94.00%	5.20%	0.79%	0.00%	NA
Japonica Intermediate	241	71.80%	24.90%	3.32%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0703531849	A -> T	LOC_Os07g07140.1	downstream_gene_variant ; 2176.0bp to feature; MODIFIER	silent_mutation	Average:55.41; most accessible tissue: Zhenshan97 root, score: 77.09	N	N	N	N
vg0703531849	A -> T	LOC_Os07g07140-LOC_Os07g07150	intergenic_region ; MODIFIER	silent_mutation	Average:55.41; most accessible tissue: Zhenshan97 root, score: 77.09	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0703531849	4.84E-07	4.82E-07	mr1919_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