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Detailed information for vg0825726642:

Variant ID: vg0825726642 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25726642
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTACCTTCAAAATTCCGTCTCCATCGGAATATTTGTACCCTTTGCGATCAAGAGTACATAAAGAGATGAGACTTCTCTTCAAATTTGGAATATGCCGCA[C/T]
ATCTGACAATGTTCTAATACAGCCATCAAACATCTCGTTCTGAACTGTTCCAATACCTGCAACCTCGCATGGTGTATCATCACCCATCAAAACAGTACCA

Reverse complement sequence

TGGTACTGTTTTGATGGGTGATGATACACCATGCGAGGTTGCAGGTATTGGAACAGTTCAGAACGAGATGTTTGATGGCTGTATTAGAACATTGTCAGAT[G/A]
TGCGGCATATTCCAAATTTGAAGAGAAGTCTCATCTCTTTATGTACTCTTGATCGCAAAGGGTACAAATATTCCGATGGAGACGGAATTTTGAAGGTAAC

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	94.80%	4.80%	0.38%	0.00%	NA
All Indica	2759	98.90%	0.90%	0.18%	0.00%	NA
All Japonica	1512	89.60%	9.80%	0.66%	0.00%	NA
Aus	269	85.10%	14.10%	0.74%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	98.70%	1.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.30%	0.38%	0.00%	NA
Temperate Japonica	767	99.50%	0.40%	0.13%	0.00%	NA
Tropical Japonica	504	74.00%	24.80%	1.19%	0.00%	NA
Japonica Intermediate	241	90.50%	8.30%	1.24%	0.00%	NA
VI/Aromatic	96	92.70%	6.20%	1.04%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg0825726642	C -> T	LOC_Os08g40640.1	missense_variant ; p.Val710Met; MODERATE	nonsynonymous_codon ; V710I	Average:31.065; most accessible tissue: Minghui63 root, score: 45.031	benign	1.281	DELETERIOUS	0.00
vg0825726642	C -> T	LOC_Os08g40640.1	missense_variant ; p.Val710Met; MODERATE	nonsynonymous_codon ; V710M	Average:31.065; most accessible tissue: Minghui63 root, score: 45.031	benign	1.081	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825726642	3.70E-06	3.70E-06	mr1369_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
vg0825726642	4.85E-06	4.85E-06	mr1453_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