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Detailed information for vg0412820231:

Variant ID: vg0412820231 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12820231
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 47. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGCAATCCTTTTCCTGTCAATATGGTACATACAGCTGGTCGAACAGCCGATGGAGGAAAAGCTCGAGGTTTTCAAATGAACTCGGCTATGATTATCAA[T/C]
AAGTATCAGAGGAAATATGATTAGCATCAGGAAAAGTATTATGAGGAAGATGATAGCGGTCTTGATCCTCATTGGGGTTGTGAGTTCTTTAGATTCTGTT

Reverse complement sequence

AACAGAATCTAAAGAACTCACAACCCCAATGAGGATCAAGACCGCTATCATCTTCCTCATAATACTTTTCCTGATGCTAATCATATTTCCTCTGATACTT[A/G]
TTGATAATCATAGCCGAGTTCATTTGAAAACCTCGAGCTTTTCCTCCATCGGCTGTTCGACCAGCTGTATGTACCATATTGACAGGAAAAGGATTGCCAT

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	52.70%	39.40%	6.05%	1.84%	NA
All Indica	2759	28.20%	61.50%	7.68%	2.65%	NA
All Japonica	1512	99.10%	0.30%	0.40%	0.20%	NA
Aus	269	23.40%	50.20%	23.42%	2.97%	NA
Indica I	595	55.60%	38.20%	4.03%	2.18%	NA
Indica II	465	35.30%	57.20%	6.02%	1.51%	NA
Indica III	913	3.30%	82.80%	11.17%	2.74%	NA
Indica Intermediate	786	32.10%	57.00%	7.38%	3.56%	NA
Temperate Japonica	767	99.60%	0.10%	0.13%	0.13%	NA
Tropical Japonica	504	99.40%	0.20%	0.20%	0.20%	NA
Japonica Intermediate	241	97.10%	0.80%	1.66%	0.41%	NA
VI/Aromatic	96	93.80%	4.20%	2.08%	0.00%	NA
Intermediate	90	67.80%	25.60%	3.33%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412820231	T -> C	LOC_Os04g22620.1	upstream_gene_variant ; 4502.0bp to feature; MODIFIER	silent_mutation	Average:17.229; most accessible tissue: Callus, score: 44.194	N	N	N	N
vg0412820231	T -> C	LOC_Os04g22640.1	downstream_gene_variant ; 4164.0bp to feature; MODIFIER	silent_mutation	Average:17.229; most accessible tissue: Callus, score: 44.194	N	N	N	N
vg0412820231	T -> C	LOC_Os04g22630.1	intron_variant ; MODIFIER	silent_mutation	Average:17.229; most accessible tissue: Callus, score: 44.194	N	N	N	N
vg0412820231	T -> DEL	N	N	silent_mutation	Average:17.229; most accessible tissue: Callus, score: 44.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412820231	9.22E-09	NA	mr1707_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
vg0412820231	2.94E-07	NA	mr1707_2	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
vg0412820231	4.47E-06	NA	mr1860_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