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Detailed information for vg0722262097:

Variant ID: vg0722262097 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 22262097
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, T: 0.06, others allele: 0.00, population size: 163. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGGAATTTAGAGAGAGAGACACAAGACAAGTTTCTCATGAGGTTAGACCTCAGGTTAGATATCCTCTAAAAATTCCTATGAATCGAAGCAATCCATAG[G/T]
ATTTCAGGAGGGTCATTCCTTTGTTCCAAATGAGTATTCTATTAGAATCCTCCAAAATCCCTTAAAAATCCTTCCTTCTAAAGGAGCCCTTAAAGATGGC

Reverse complement sequence

GCCATCTTTAAGGGCTCCTTTAGAAGGAAGGATTTTTAAGGGATTTTGGAGGATTCTAATAGAATACTCATTTGGAACAAAGGAATGACCCTCCTGAAAT[C/A]
CTATGGATTGCTTCGATTCATAGGAATTTTTAGAGGATATCTAACCTGAGGTCTAACCTCATGAGAAACTTGTCTTGTGTCTCTCTCTCTAAATTCCTTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.30%	38.40%	0.30%	0.02%	NA
All Indica	2759	87.50%	12.10%	0.40%	0.04%	NA
All Japonica	1512	6.40%	93.50%	0.13%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	78.10%	20.90%	0.86%	0.22%	NA
Indica III	913	85.90%	13.80%	0.33%	0.00%	NA
Indica Intermediate	786	85.80%	13.90%	0.38%	0.00%	NA
Temperate Japonica	767	0.30%	99.60%	0.13%	0.00%	NA
Tropical Japonica	504	14.30%	85.70%	0.00%	0.00%	NA
Japonica Intermediate	241	9.50%	90.00%	0.41%	0.00%	NA
VI/Aromatic	96	70.80%	29.20%	0.00%	0.00%	NA
Intermediate	90	55.60%	43.30%	1.11%	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
vg0722262097	G -> DEL	N	N	silent_mutation	Average:31.895; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0722262097	G -> T	LOC_Os07g37156.1	upstream_gene_variant ; 3644.0bp to feature; MODIFIER	silent_mutation	Average:31.895; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N
vg0722262097	G -> T	LOC_Os07g37156-LOC_Os07g37180	intergenic_region ; MODIFIER	silent_mutation	Average:31.895; most accessible tissue: Minghui63 panicle, score: 46.754	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0722262097	NA	1.18E-06	mr1124	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
vg0722262097	7.05E-08	7.05E-08	mr1542	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
vg0722262097	4.32E-06	4.32E-06	mr1795	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
vg0722262097	NA	4.72E-13	mr1949	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
vg0722262097	NA	1.35E-23	mr1949_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