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Detailed information for vg0906086651:

Variant ID: vg0906086651 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6086651
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAAAGTTTATATACCTGATTCAAATTTGAATTTGAATTATATCCGATTCAAATTTGAATTTGAATTCAAACATTTTTTATATATAGTATTTCTATACAT[C/A]
TAAAGTTTATACACCTAAAGTTTATAGACCCAAAGTTTATAAGTCAAAAGTTTACATGCCCGATTCAAATTTAAATTTGAATTCAAATATTAGTTTATAG

Reverse complement sequence

CTATAAACTAATATTTGAATTCAAATTTAAATTTGAATCGGGCATGTAAACTTTTGACTTATAAACTTTGGGTCTATAAACTTTAGGTGTATAAACTTTA[G/T]
ATGTATAGAAATACTATATATAAAAAATGTTTGAATTCAAATTCAAATTTGAATCGGATATAATTCAAATTCAAATTTGAATCAGGTATATAAACTTTTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.70%	3.70%	0.38%	1.18%	NA
All Indica	2759	93.30%	4.70%	0.58%	1.38%	NA
All Japonica	1512	96.50%	2.30%	0.13%	1.06%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	90.10%	9.60%	0.17%	0.17%	NA
Indica II	465	94.80%	0.00%	1.08%	4.09%	NA
Indica III	913	96.30%	3.40%	0.22%	0.11%	NA
Indica Intermediate	786	91.50%	5.30%	1.02%	2.16%	NA
Temperate Japonica	767	96.60%	1.20%	0.13%	2.09%	NA
Tropical Japonica	504	98.60%	1.20%	0.20%	0.00%	NA
Japonica Intermediate	241	91.70%	8.30%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906086651	C -> DEL	N	N	silent_mutation	Average:15.231; most accessible tissue: Minghui63 flower, score: 23.1	N	N	N	N
vg0906086651	C -> A	LOC_Os09g11000.1	upstream_gene_variant ; 1961.0bp to feature; MODIFIER	silent_mutation	Average:15.231; most accessible tissue: Minghui63 flower, score: 23.1	N	N	N	N
vg0906086651	C -> A	LOC_Os09g11000-LOC_Os09g11005	intergenic_region ; MODIFIER	silent_mutation	Average:15.231; most accessible tissue: Minghui63 flower, score: 23.1	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906086651	4.98E-07	1.27E-07	mr1768	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