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Detailed information for vg0905542148:

Variant ID: vg0905542148 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5542148
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAATATAAGAGATTTTGATATTTTGTTTACACTGTTTGACCTTTCGTCTTATTAAAAAATTTTTAGAATTATTATTAATTTTATTTGTGACTTACTTTA[G/A]
GACACGACTCCTGGTCGGGCGCCCGATCGAGAGGGAGTCAAATCGGCGTCACTCATACGTGCAAAACCACTTTAAACTATTTTTTCTCTTAAATTACTTA

Reverse complement sequence

TAAGTAATTTAAGAGAAAAAATAGTTTAAAGTGGTTTTGCACGTATGAGTGACGCCGATTTGACTCCCTCTCGATCGGGCGCCCGACCAGGAGTCGTGTC[C/T]
TAAAGTAAGTCACAAATAAAATTAATAATAATTCTAAAAATTTTTTAATAAGACGAAAGGTCAAACAGTGTAAACAAAATATCAAAATCTCTTATATTAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.10%	1.30%	0.93%	11.64%	NA
All Indica	2759	91.80%	2.30%	0.91%	4.97%	NA
All Japonica	1512	84.30%	0.00%	0.86%	14.81%	NA
Aus	269	58.40%	0.00%	1.49%	40.15%	NA
Indica I	595	89.20%	7.70%	1.18%	1.85%	NA
Indica II	465	94.80%	0.00%	0.65%	4.52%	NA
Indica III	913	95.40%	0.00%	0.77%	3.83%	NA
Indica Intermediate	786	87.90%	2.20%	1.02%	8.91%	NA
Temperate Japonica	767	93.40%	0.00%	0.65%	6.00%	NA
Tropical Japonica	504	83.90%	0.00%	0.60%	15.48%	NA
Japonica Intermediate	241	56.40%	0.00%	2.07%	41.49%	NA
VI/Aromatic	96	22.90%	0.00%	1.04%	76.04%	NA
Intermediate	90	90.00%	0.00%	1.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0905542148	G -> DEL	N	N	silent_mutation	Average:28.711; most accessible tissue: Callus, score: 33.406	N	N	N	N
vg0905542148	G -> A	LOC_Os09g10180.1	upstream_gene_variant ; 2217.0bp to feature; MODIFIER	silent_mutation	Average:28.711; most accessible tissue: Callus, score: 33.406	N	N	N	N
vg0905542148	G -> A	LOC_Os09g10190.1	upstream_gene_variant ; 903.0bp to feature; MODIFIER	silent_mutation	Average:28.711; most accessible tissue: Callus, score: 33.406	N	N	N	N
vg0905542148	G -> A	LOC_Os09g10180-LOC_Os09g10190	intergenic_region ; MODIFIER	silent_mutation	Average:28.711; most accessible tissue: Callus, score: 33.406	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905542148	9.88E-07	1.35E-08	mr1563	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