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Detailed information for vg0913385027:

Variant ID: vg0913385027 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 13385027
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAATTTTGCACTTTGCATTTCAATCCCTATAATATTCATATTTACATTTGAGTCTCTGTTCGAGGTTAGTGGTCAGTTCTTGTTTAAAAAATAAAAAAAA[T/G]
AAAAAAAGAAAATGCAGAAAGGTGCAAAGAAAAAGAAAGAAAAAAGCCGCACCTAAAAAAAGAAAAAAAAAGGCAAAAAGGTGCTTAAAAAAAGCCGCAC

Reverse complement sequence

GTGCGGCTTTTTTTAAGCACCTTTTTGCCTTTTTTTTTCTTTTTTTAGGTGCGGCTTTTTTCTTTCTTTTTCTTTGCACCTTTCTGCATTTTCTTTTTTT[A/C]
TTTTTTTTATTTTTTAAACAAGAACTGACCACTAACCTCGAACAGAGACTCAAATGTAAATATGAATATTATAGGGATTGAAATGCAAAGTGCAAAATTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.40%	1.80%	2.75%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	86.10%	5.60%	8.27%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	74.80%	10.00%	15.12%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	93.80%	2.90%	3.32%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	0.00%	4.44%	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
vg0913385027	T -> G	LOC_Os09g22090.1	upstream_gene_variant ; 3510.0bp to feature; MODIFIER	silent_mutation	Average:26.453; most accessible tissue: Callus, score: 41.481	N	N	N	N
vg0913385027	T -> G	LOC_Os09g22100.1	intron_variant ; MODIFIER	silent_mutation	Average:26.453; most accessible tissue: Callus, score: 41.481	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0913385027	2.53E-06	NA	mr1672_2	Jap_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