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Detailed information for vg0312940183:

Variant ID: vg0312940183 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 12940183
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTAAACTCGCAAATCGACCATTCATGTCCTCAAACTTGTTTGACTGTGTCATCCTGGTCCCTAAACTTGCAGATCACTCGTTTAGGTCCTCCAACTTATT[C/T]
AGTTATGTCACCCGGTCCCTAAACTTGGATTTGAATATCATCTGGGTCAAATAGGACGGTATAAAAACTTTATATTTAAAAATAATTCATATTTTTTTCA

Reverse complement sequence

TGAAAAAAATATGAATTATTTTTAAATATAAAGTTTTTATACCGTCCTATTTGACCCAGATGATATTCAAATCCAAGTTTAGGGACCGGGTGACATAACT[G/A]
AATAAGTTGGAGGACCTAAACGAGTGATCTGCAAGTTTAGGGACCAGGATGACACAGTCAAACAAGTTTGAGGACATGAATGGTCGATTTGCGAGTTTAG

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	40.10%	36.20%	4.59%	19.13%	NA
All Indica	2759	63.20%	6.30%	6.13%	24.39%	NA
All Japonica	1512	6.30%	91.80%	1.79%	0.13%	NA
Aus	269	6.30%	9.30%	5.20%	79.18%	NA
Indica I	595	70.90%	2.00%	14.29%	12.77%	NA
Indica II	465	81.30%	3.00%	4.30%	11.40%	NA
Indica III	913	51.90%	10.10%	2.19%	35.82%	NA
Indica Intermediate	786	59.80%	7.00%	5.60%	27.61%	NA
Temperate Japonica	767	1.80%	97.10%	1.04%	0.00%	NA
Tropical Japonica	504	4.20%	93.50%	1.98%	0.40%	NA
Japonica Intermediate	241	24.90%	71.40%	3.73%	0.00%	NA
VI/Aromatic	96	8.30%	84.40%	2.08%	5.21%	NA
Intermediate	90	33.30%	48.90%	5.56%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0312940183	C -> T	LOC_Os03g22530.1	upstream_gene_variant ; 1783.0bp to feature; MODIFIER	silent_mutation	Average:29.624; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N
vg0312940183	C -> T	LOC_Os03g22510-LOC_Os03g22530	intergenic_region ; MODIFIER	silent_mutation	Average:29.624; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N
vg0312940183	C -> DEL	N	N	silent_mutation	Average:29.624; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0312940183	4.17E-06	4.17E-06	mr1908	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
vg0312940183	NA	1.49E-07	mr1133_2	Ind_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
vg0312940183	NA	7.01E-07	mr1212_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