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Detailed information for vg0903264298:

Variant ID: vg0903264298 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 3264298
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAACTCTTTGGACCGCCGGTCAGCATACATCCATTGCCGATCCATCTACATAAGTCCAAAAAAAATCGTACACAAATAATTATTCTTACAATAATGACAG[T/C]
CATACAATAATTACAAGATAATTACAAACTGTTTCAACAGTCATACAATAATGACATATCTTTATTCATACAAAAATCATAAAATATTACACCAAATAAT

Reverse complement sequence

ATTATTTGGTGTAATATTTTATGATTTTTGTATGAATAAAGATATGTCATTATTGTATGACTGTTGAAACAGTTTGTAATTATCTTGTAATTATTGTATG[A/G]
CTGTCATTATTGTAAGAATAATTATTTGTGTACGATTTTTTTTGGACTTATGTAGATGGATCGGCAATGGATGTATGCTGACCGGCGGTCCAAAGAGTTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.80%	6.40%	1.78%	11.00%	NA
All Indica	2759	95.10%	4.00%	0.54%	0.36%	NA
All Japonica	1512	66.00%	0.10%	3.37%	30.49%	NA
Aus	269	26.00%	69.90%	4.09%	0.00%	NA
Indica I	595	99.50%	0.00%	0.00%	0.50%	NA
Indica II	465	93.30%	5.80%	0.86%	0.00%	NA
Indica III	913	96.40%	2.80%	0.44%	0.33%	NA
Indica Intermediate	786	91.50%	7.10%	0.89%	0.51%	NA
Temperate Japonica	767	98.00%	0.00%	0.26%	1.69%	NA
Tropical Japonica	504	23.00%	0.00%	8.33%	68.65%	NA
Japonica Intermediate	241	53.90%	0.80%	2.90%	42.32%	NA
VI/Aromatic	96	55.20%	3.10%	3.12%	38.54%	NA
Intermediate	90	81.10%	1.10%	4.44%	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
vg0903264298	T -> DEL	N	N	silent_mutation	Average:17.212; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0903264298	T -> C	LOC_Os09g06820.1	upstream_gene_variant ; 373.0bp to feature; MODIFIER	silent_mutation	Average:17.212; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0903264298	T -> C	LOC_Os09g06830.1	downstream_gene_variant ; 2647.0bp to feature; MODIFIER	silent_mutation	Average:17.212; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0903264298	T -> C	LOC_Os09g06820-LOC_Os09g06830	intergenic_region ; MODIFIER	silent_mutation	Average:17.212; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0903264298	NA	9.08E-08	mr1642_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
vg0903264298	NA	4.86E-07	mr1808_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0903264298	NA	5.31E-07	mr1815_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251