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Detailed information for vg1220323426:

Variant ID: vg1220323426 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20323426
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 141. )

Flanking Sequence (100 bp) in Reference Genome:

GAGACAGTTGATGGCAAGTTAGAAGTGAATGACAAGCATGATATTCTTATGATGACAAACATAGTATCCTAGTAATGACAAGCAGGTTACGACGCATGAC[A/G]
TGAAGTTGATAACTTGTCCGAGGTTGACTCCGAAGATATGAATCATGAGAAGTTCTGGAACGGAAGCATCACTGAACTACCGCAACCTAGTCTGAGTCAG

Reverse complement sequence

CTGACTCAGACTAGGTTGCGGTAGTTCAGTGATGCTTCCGTTCCAGAACTTCTCATGATTCATATCTTCGGAGTCAACCTCGGACAAGTTATCAACTTCA[T/C]
GTCATGCGTCGTAACCTGCTTGTCATTACTAGGATACTATGTTTGTCATCATAAGAATATCATGCTTGTCATTCACTTCTAACTTGCCATCAACTGTCTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.30%	2.30%	6.67%	45.75%	NA
All Indica	2759	27.50%	2.20%	5.44%	64.84%	NA
All Japonica	1512	82.70%	0.00%	3.11%	14.15%	NA
Aus	269	21.20%	16.40%	34.94%	27.51%	NA
Indica I	595	47.90%	0.70%	6.72%	44.71%	NA
Indica II	465	40.20%	1.30%	6.02%	52.47%	NA
Indica III	913	3.70%	2.80%	3.29%	90.14%	NA
Indica Intermediate	786	32.20%	3.20%	6.62%	58.02%	NA
Temperate Japonica	767	97.40%	0.00%	0.39%	2.22%	NA
Tropical Japonica	504	56.90%	0.00%	7.94%	35.12%	NA
Japonica Intermediate	241	90.00%	0.00%	1.66%	8.30%	NA
VI/Aromatic	96	29.20%	1.00%	17.71%	52.08%	NA
Intermediate	90	52.20%	1.10%	7.78%	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
vg1220323426	A -> DEL	N	N	silent_mutation	Average:16.12; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg1220323426	A -> G	LOC_Os12g33660.1	downstream_gene_variant ; 1970.0bp to feature; MODIFIER	silent_mutation	Average:16.12; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg1220323426	A -> G	LOC_Os12g33670.1	downstream_gene_variant ; 3421.0bp to feature; MODIFIER	silent_mutation	Average:16.12; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg1220323426	A -> G	LOC_Os12g33660-LOC_Os12g33670	intergenic_region ; MODIFIER	silent_mutation	Average:16.12; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220323426	NA	4.10E-10	mr1216	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