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Detailed information for vg0826973911:

Variant ID: vg0826973911 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 26973911
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGTTAAAAATAATCCTCGAATAGTCTCAAGTATCACTTTAACTTTCTGATTGGTGTTCATAGTTTTGTTCACATTTGTTTTCGCTAACCTTGGATACAG[T/A]
AGATGGTATATATATTTGATTTCCATCTTTAATCCCAAAACTTGTGGATTACGGGCTTTACTAAAACTTGTGCGTGTGTGTGCATATTGCCTTTTCAACC

Reverse complement sequence

GGTTGAAAAGGCAATATGCACACACACGCACAAGTTTTAGTAAAGCCCGTAATCCACAAGTTTTGGGATTAAAGATGGAAATCAAATATATATACCATCT[A/T]
CTGTATCCAAGGTTAGCGAAAACAAATGTGAACAAAACTATGAACACCAATCAGAAAGTTAAAGTGATACTTGAGACTATTCGAGGATTATTTTTAACAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.30%	24.10%	0.36%	37.26%	NA
All Indica	2759	7.80%	39.30%	0.47%	52.48%	NA
All Japonica	1512	96.60%	2.20%	0.00%	1.19%	NA
Aus	269	7.80%	0.00%	1.49%	90.71%	NA
Indica I	595	3.00%	56.50%	0.34%	40.17%	NA
Indica II	465	24.70%	46.70%	0.43%	28.17%	NA
Indica III	913	2.70%	26.90%	0.33%	69.99%	NA
Indica Intermediate	786	7.30%	36.10%	0.76%	55.85%	NA
Temperate Japonica	767	96.30%	2.90%	0.00%	0.78%	NA
Tropical Japonica	504	97.60%	1.00%	0.00%	1.39%	NA
Japonica Intermediate	241	95.40%	2.50%	0.00%	2.07%	NA
VI/Aromatic	96	79.20%	1.00%	0.00%	19.79%	NA
Intermediate	90	38.90%	25.60%	0.00%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0826973911	T -> A	LOC_Os08g42670.1	intron_variant ; MODIFIER	silent_mutation	Average:26.147; most accessible tissue: Zhenshan97 young leaf, score: 52.657	N	N	N	N
vg0826973911	T -> A	LOC_Os08g42670.2	intron_variant ; MODIFIER	silent_mutation	Average:26.147; most accessible tissue: Zhenshan97 young leaf, score: 52.657	N	N	N	N
vg0826973911	T -> DEL	N	N	silent_mutation	Average:26.147; most accessible tissue: Zhenshan97 young leaf, score: 52.657	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0826973911	NA	1.33E-06	mr1245	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
vg0826973911	NA	4.53E-11	mr1352	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
vg0826973911	NA	6.93E-06	mr1740	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
vg0826973911	NA	9.52E-10	mr1881	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
vg0826973911	NA	2.24E-23	mr1943	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
vg0826973911	NA	8.70E-06	mr1943	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
vg0826973911	NA	4.64E-06	mr1956	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