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Detailed information for vg0712655383:

Variant ID: vg0712655383 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 12655383
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATCATATAGATAAAACAAGAATTTTATCTCCACTTGGTTCTGCAAGGATAGTACATAAGTGACAATCTCATCCAAAATTGTTTCTTCTCACTAACAGGG[G/C]
CTCTAATAAAGTGGAGAATTCGATAATCTGATTCCTCTTGTAAATAGCTACAATTTATCATTATGAAGGATGAAAAAAATAGTTTCATTGTCAGAGATCG

Reverse complement sequence

CGATCTCTGACAATGAAACTATTTTTTTCATCCTTCATAATGATAAATTGTAGCTATTTACAAGAGGAATCAGATTATCGAATTCTCCACTTTATTAGAG[C/G]
CCCTGTTAGTGAGAAGAAACAATTTTGGATGAGATTGTCACTTATGTACTATCCTTGCAGAACCAAGTGGAGATAAAATTCTTGTTTTATCTATATGATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.00%	15.20%	0.51%	57.30%	NA
All Indica	2759	9.40%	0.50%	0.72%	89.45%	NA
All Japonica	1512	50.90%	45.40%	0.00%	3.70%	NA
Aus	269	48.30%	0.00%	1.12%	50.56%	NA
Indica I	595	0.20%	0.20%	1.01%	98.66%	NA
Indica II	465	7.10%	1.30%	0.86%	90.75%	NA
Indica III	913	10.10%	0.20%	0.33%	89.38%	NA
Indica Intermediate	786	16.80%	0.50%	0.89%	81.81%	NA
Temperate Japonica	767	74.10%	24.40%	0.00%	1.56%	NA
Tropical Japonica	504	23.60%	69.60%	0.00%	6.75%	NA
Japonica Intermediate	241	34.40%	61.40%	0.00%	4.15%	NA
VI/Aromatic	96	86.50%	0.00%	0.00%	13.54%	NA
Intermediate	90	41.10%	18.90%	1.11%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0712655383	G -> DEL	N	N	silent_mutation	Average:10.152; most accessible tissue: Callus, score: 53.177	N	N	N	N
vg0712655383	G -> C	LOC_Os07g22496.1	upstream_gene_variant ; 4487.0bp to feature; MODIFIER	silent_mutation	Average:10.152; most accessible tissue: Callus, score: 53.177	N	N	N	N
vg0712655383	G -> C	LOC_Os07g22494.1	intron_variant ; MODIFIER	silent_mutation	Average:10.152; most accessible tissue: Callus, score: 53.177	N	N	N	N
vg0712655383	G -> C	LOC_Os07g22494.4	intron_variant ; MODIFIER	silent_mutation	Average:10.152; most accessible tissue: Callus, score: 53.177	N	N	N	N
vg0712655383	G -> C	LOC_Os07g22494.2	intron_variant ; MODIFIER	silent_mutation	Average:10.152; most accessible tissue: Callus, score: 53.177	N	N	N	N
vg0712655383	G -> C	LOC_Os07g22494.3	intron_variant ; MODIFIER	silent_mutation	Average:10.152; most accessible tissue: Callus, score: 53.177	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0712655383	NA	4.15E-06	mr1928	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
vg0712655383	8.15E-07	5.43E-08	mr1928	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
vg0712655383	NA	1.86E-10	mr1761_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