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Detailed information for vg0907147216:

Variant ID: vg0907147216 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7147216
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATAAATTATGATTTTTATGATTTTAATATAAAAATAGCATTTTTTTTTACTTGTATGACACCAAGTTACTGATAAATGTCAACAAGTACAAGAACATA[T/C]
ATTTGGATGTTAAAAATAAGGGGGGATCAATTAAAATTGGGTTATATTGTCAGCAAGGGGTATATTAACCAGTACTGATAGCTGAGGGGTGTAAACTAGT

Reverse complement sequence

ACTAGTTTACACCCCTCAGCTATCAGTACTGGTTAATATACCCCTTGCTGACAATATAACCCAATTTTAATTGATCCCCCCTTATTTTTAACATCCAAAT[A/G]
TATGTTCTTGTACTTGTTGACATTTATCAGTAACTTGGTGTCATACAAGTAAAAAAAAATGCTATTTTTATATTAAAATCATAAAAATCATAATTTATAT

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	95.90%	4.00%	0.11%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	90.30%	9.40%	0.33%	0.00%	NA
Aus	269	99.60%	0.40%	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	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	82.90%	16.40%	0.65%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	93.40%	6.60%	0.00%	0.00%	NA
VI/Aromatic	96	63.50%	36.50%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	0.00%	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
vg0907147216	T -> C	LOC_Os09g12480.1	upstream_gene_variant ; 1238.0bp to feature; MODIFIER	silent_mutation	Average:41.091; most accessible tissue: Callus, score: 68.146	N	N	N	N
vg0907147216	T -> C	LOC_Os09g12490.1	downstream_gene_variant ; 4108.0bp to feature; MODIFIER	silent_mutation	Average:41.091; most accessible tissue: Callus, score: 68.146	N	N	N	N
vg0907147216	T -> C	LOC_Os09g12480-LOC_Os09g12490	intergenic_region ; MODIFIER	silent_mutation	Average:41.091; most accessible tissue: Callus, score: 68.146	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907147216	3.68E-06	6.42E-14	mr1070	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
vg0907147216	NA	1.20E-11	mr1128	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