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Detailed information for vg0726174758:

Variant ID: vg0726174758 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 26174758
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

ACAGAGGCTCATTCAGATTTGTAGTATTAAAATATATCTAGATTCATAGGGTCTGTTTGGTACAGCTCCAACTCCTAAATTTAACTCCAGGAGTTGAGTC[T/C]
GGAGTGGAGTTGTGGAGCTGTCTAAACCCAGCTCCACAACTCTAGTTCATTTTGTGAGAGCTCCACTACCAGTTTTGGTGGAGCTGAAACTGTTTGGCTG

Reverse complement sequence

CAGCCAAACAGTTTCAGCTCCACCAAAACTGGTAGTGGAGCTCTCACAAAATGAACTAGAGTTGTGGAGCTGGGTTTAGACAGCTCCACAACTCCACTCC[A/G]
GACTCAACTCCTGGAGTTAAATTTAGGAGTTGGAGCTGTACCAAACAGACCCTATGAATCTAGATATATTTTAATACTACAAATCTGAATGAGCCTCTGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.90%	9.00%	0.11%	0.00%	NA
All Indica	2759	86.70%	13.20%	0.18%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	78.40%	21.60%	0.00%	0.00%	NA
Indica I	595	98.70%	1.30%	0.00%	0.00%	NA
Indica II	465	93.50%	6.50%	0.00%	0.00%	NA
Indica III	913	76.90%	23.00%	0.11%	0.00%	NA
Indica Intermediate	786	84.90%	14.60%	0.51%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0726174758	T -> C	LOC_Os07g43750.1	upstream_gene_variant ; 1820.0bp to feature; MODIFIER	silent_mutation	Average:65.939; most accessible tissue: Minghui63 root, score: 83.399	N	N	N	N
vg0726174758	T -> C	LOC_Os07g43730.1	downstream_gene_variant ; 2202.0bp to feature; MODIFIER	silent_mutation	Average:65.939; most accessible tissue: Minghui63 root, score: 83.399	N	N	N	N
vg0726174758	T -> C	LOC_Os07g43740.1	downstream_gene_variant ; 372.0bp to feature; MODIFIER	silent_mutation	Average:65.939; most accessible tissue: Minghui63 root, score: 83.399	N	N	N	N
vg0726174758	T -> C	LOC_Os07g43740-LOC_Os07g43750	intergenic_region ; MODIFIER	silent_mutation	Average:65.939; most accessible tissue: Minghui63 root, score: 83.399	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0726174758	NA	8.42E-06	mr1107	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
vg0726174758	NA	4.11E-07	mr1226	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
vg0726174758	NA	1.88E-06	mr1144_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
vg0726174758	NA	5.85E-08	mr1155_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
vg0726174758	NA	4.60E-06	mr1168_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
vg0726174758	4.17E-06	NA	mr1198_2	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
vg0726174758	NA	2.87E-06	mr1620_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