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Detailed information for vg0909394181:

Variant ID: vg0909394181 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9394181
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACACATATGGATGTTTGTTTTTTTCTTTTTTTTCTTTTCGGACAAATATTTGTTTATCATAGGAATAGGGCGTGCGTATTTGTATTCATAATGTGCGTC[C/T]
GCACGCATTTATATGAGCTCATGTGATTGCCTTTTAAATTGTTAGTAAAAAAAGTATTTTTAAAAATTTGACAGGAAGAGGGTGGAGCAACGGGTGGCAT

Reverse complement sequence

ATGCCACCCGTTGCTCCACCCTCTTCCTGTCAAATTTTTAAAAATACTTTTTTTACTAACAATTTAAAAGGCAATCACATGAGCTCATATAAATGCGTGC[G/A]
GACGCACATTATGAATACAAATACGCACGCCCTATTCCTATGATAAACAAATATTTGTCCGAAAAGAAAAAAAAGAAAAAAACAAACATCCATATGTGTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.40%	24.50%	5.56%	42.47%	NA
All Indica	2759	5.50%	31.70%	6.09%	56.65%	NA
All Japonica	1512	70.40%	1.90%	3.11%	24.54%	NA
Aus	269	2.20%	72.90%	11.15%	13.75%	NA
Indica I	595	9.20%	24.40%	7.23%	59.16%	NA
Indica II	465	1.90%	24.10%	4.52%	69.46%	NA
Indica III	913	6.10%	42.70%	4.93%	46.22%	NA
Indica Intermediate	786	4.20%	29.00%	7.51%	59.29%	NA
Temperate Japonica	767	75.40%	1.00%	2.61%	20.99%	NA
Tropical Japonica	504	69.40%	1.20%	2.78%	26.59%	NA
Japonica Intermediate	241	56.80%	6.20%	5.39%	31.54%	NA
VI/Aromatic	96	28.10%	49.00%	9.38%	13.54%	NA
Intermediate	90	51.10%	13.30%	10.00%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909394181	C -> DEL	N	N	silent_mutation	Average:14.85; most accessible tissue: Callus, score: 37.906	N	N	N	N
vg0909394181	C -> T	LOC_Os09g15360.1	upstream_gene_variant ; 2779.0bp to feature; MODIFIER	silent_mutation	Average:14.85; most accessible tissue: Callus, score: 37.906	N	N	N	N
vg0909394181	C -> T	LOC_Os09g15370.1	upstream_gene_variant ; 4931.0bp to feature; MODIFIER	silent_mutation	Average:14.85; most accessible tissue: Callus, score: 37.906	N	N	N	N
vg0909394181	C -> T	LOC_Os09g15365.1	downstream_gene_variant ; 3325.0bp to feature; MODIFIER	silent_mutation	Average:14.85; most accessible tissue: Callus, score: 37.906	N	N	N	N
vg0909394181	C -> T	LOC_Os09g15360-LOC_Os09g15365	intergenic_region ; MODIFIER	silent_mutation	Average:14.85; most accessible tissue: Callus, score: 37.906	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909394181	3.49E-06	NA	mr1705_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