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Detailed information for vg0220727676:

Variant ID: vg0220727676 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20727676
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATATTCGTTGAAAACATATCATGAAATATATTAATGGTTAAAATATCTTCCTGAATACTGCGTAAAATAATACTCCCTCCGTTTTTAAATATTTGACG[C/T]
TGTTGACTTTTTTAAATATGTTTGACTGTTTGTCTTATTCAAAAAATTTAAGTAATTATTAATTCTTTTCCTATCATTTGATTTATTGTTAAATATACTT

Reverse complement sequence

AAGTATATTTAACAATAAATCAAATGATAGGAAAAGAATTAATAATTACTTAAATTTTTTGAATAAGACAAACAGTCAAACATATTTAAAAAAGTCAACA[G/A]
CGTCAAATATTTAAAAACGGAGGGAGTATTATTTTACGCAGTATTCAGGAAGATATTTTAACCATTAATATATTTCATGATATGTTTTCAACGAATATAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.70%	7.30%	0.08%	0.00%	NA
All Indica	2759	98.70%	1.30%	0.00%	0.00%	NA
All Japonica	1512	81.00%	18.70%	0.26%	0.00%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.50%	1.50%	0.00%	0.00%	NA
Indica III	913	98.60%	1.40%	0.00%	0.00%	NA
Indica Intermediate	786	98.10%	1.90%	0.00%	0.00%	NA
Temperate Japonica	767	74.60%	25.40%	0.00%	0.00%	NA
Tropical Japonica	504	84.10%	15.90%	0.00%	0.00%	NA
Japonica Intermediate	241	95.00%	3.30%	1.66%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	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
vg0220727676	C -> T	LOC_Os02g34570.1	downstream_gene_variant ; 596.0bp to feature; MODIFIER	silent_mutation	Average:58.832; most accessible tissue: Minghui63 root, score: 78.833	N	N	N	N
vg0220727676	C -> T	LOC_Os02g34570.2	downstream_gene_variant ; 597.0bp to feature; MODIFIER	silent_mutation	Average:58.832; most accessible tissue: Minghui63 root, score: 78.833	N	N	N	N
vg0220727676	C -> T	LOC_Os02g34560-LOC_Os02g34570	intergenic_region ; MODIFIER	silent_mutation	Average:58.832; most accessible tissue: Minghui63 root, score: 78.833	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220727676	NA	3.31E-06	mr1101	Jap_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
vg0220727676	1.88E-06	1.88E-06	mr1954_2	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