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Detailed information for vg0907264200:

Variant ID: vg0907264200 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7264200
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:

TACCCTAGTTTTAATCCATCTTTGTCGGTTTGCGCCGTAAACCGTCCGCCGCCGCTGCGAGAGTGCGACACCTCTTTGTAGATTTGTCCTGAAAACCTTC[C/T]
GTTTTGCCTATGAGACAGGTTAGTTATCCTCATATCGATCTAAATCGGCTTAGAGGCTGATTTTTGATCTCTAAATCGGCTCCGCTAACCGGTTTAGCTG

Reverse complement sequence

CAGCTAAACCGGTTAGCGGAGCCGATTTAGAGATCAAAAATCAGCCTCTAAGCCGATTTAGATCGATATGAGGATAACTAACCTGTCTCATAGGCAAAAC[G/A]
GAAGGTTTTCAGGACAAATCTACAAAGAGGTGTCGCACTCTCGCAGCGGCGGCGGACGGTTTACGGCGCAAACCGACAAAGATGGATTAAAACTAGGGTA

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	92.00%	3.70%	0.11%	4.19%	NA
All Indica	2759	86.70%	6.10%	0.14%	7.10%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	99.30%	0.00%	0.37%	0.37%	NA
Indica I	595	79.80%	19.80%	0.00%	0.34%	NA
Indica II	465	96.60%	1.70%	0.22%	1.51%	NA
Indica III	913	83.40%	0.20%	0.22%	16.21%	NA
Indica Intermediate	786	89.80%	5.10%	0.13%	4.96%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	98.90%	1.10%	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
vg0907264200	C -> DEL	N	N	silent_mutation	Average:30.603; most accessible tissue: Minghui63 root, score: 50.524	N	N	N	N
vg0907264200	C -> T	LOC_Os09g12690.1	upstream_gene_variant ; 1224.0bp to feature; MODIFIER	silent_mutation	Average:30.603; most accessible tissue: Minghui63 root, score: 50.524	N	N	N	N
vg0907264200	C -> T	LOC_Os09g12700.1	upstream_gene_variant ; 3367.0bp to feature; MODIFIER	silent_mutation	Average:30.603; most accessible tissue: Minghui63 root, score: 50.524	N	N	N	N
vg0907264200	C -> T	LOC_Os09g12680-LOC_Os09g12690	intergenic_region ; MODIFIER	silent_mutation	Average:30.603; most accessible tissue: Minghui63 root, score: 50.524	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907264200	7.81E-07	9.90E-09	mr1172_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
vg0907264200	9.14E-06	7.29E-06	mr1172_2	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
vg0907264200	3.76E-06	NA	mr1536_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