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Detailed information for vg0920193418:

Variant ID: vg0920193418 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 20193418
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.27, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

TCGAGAAATGTAAACATTAATGAATGACTTAGGTACGAGGAATAACTATTAGCCTGTTTAAATGGATGATAAGTAAAATTACTTATCATTGTTCATTGTA[C/T]
CAAGATAAAATATAACTTACCAAAAATAGATAGAGAATAATCGAACTTAAAATAGTTTAACTTTTACCATCTTATAACCTAAAGCGAAGGGAGTAGCATT

Reverse complement sequence

AATGCTACTCCCTTCGCTTTAGGTTATAAGATGGTAAAAGTTAAACTATTTTAAGTTCGATTATTCTCTATCTATTTTTGGTAAGTTATATTTTATCTTG[G/A]
TACAATGAACAATGATAAGTAATTTTACTTATCATCCATTTAAACAGGCTAATAGTTATTCCTCGTACCTAAGTCATTCATTAATGTTTACATTTCTCGA

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	71.70%	13.50%	4.91%	9.84%	NA
All Indica	2759	63.80%	22.70%	8.16%	5.29%	NA
All Japonica	1512	98.10%	0.30%	0.00%	1.59%	NA
Aus	269	5.60%	0.40%	0.74%	93.31%	NA
Indica I	595	58.70%	16.30%	17.82%	7.23%	NA
Indica II	465	34.40%	52.30%	12.47%	0.86%	NA
Indica III	913	79.20%	14.50%	0.99%	5.37%	NA
Indica Intermediate	786	67.30%	19.70%	6.62%	6.36%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	97.80%	0.00%	0.00%	2.18%	NA
Japonica Intermediate	241	93.80%	0.80%	0.00%	5.39%	NA
VI/Aromatic	96	59.40%	0.00%	1.04%	39.58%	NA
Intermediate	90	81.10%	7.80%	4.44%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0920193418	C -> DEL	N	N	silent_mutation	Average:59.957; most accessible tissue: Minghui63 root, score: 77.009	N	N	N	N
vg0920193418	C -> T	LOC_Os09g34214.1	upstream_gene_variant ; 3290.0bp to feature; MODIFIER	silent_mutation	Average:59.957; most accessible tissue: Minghui63 root, score: 77.009	N	N	N	N
vg0920193418	C -> T	LOC_Os09g34200.1	downstream_gene_variant ; 1833.0bp to feature; MODIFIER	silent_mutation	Average:59.957; most accessible tissue: Minghui63 root, score: 77.009	N	N	N	N
vg0920193418	C -> T	LOC_Os09g34200-LOC_Os09g34214	intergenic_region ; MODIFIER	silent_mutation	Average:59.957; most accessible tissue: Minghui63 root, score: 77.009	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0920193418	NA	2.77E-07	mr1557	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
vg0920193418	NA	5.56E-06	mr1786	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