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Detailed information for vg0817490978:

Variant ID: vg0817490978 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17490978
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.56, G: 0.44, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TGGTCGATGGCACAATAGCTGAGCATCAAACTACGGGGCCAGTCTATTTACCAGGGGGTGTTTTCCCGAACTGCAGGCCTTTGGTCACAAGCAACCAACA[T/G]
AGTGCTTCTAGTGTACCACCAGTTCAGCCGACGGCACCGGTTTCAGCTCCTGCACCAGCTGCACCATCGCTAGCACAAAGGCAAATGACCAATCCTCGAT

Reverse complement sequence

ATCGAGGATTGGTCATTTGCCTTTGTGCTAGCGATGGTGCAGCTGGTGCAGGAGCTGAAACCGGTGCCGTCGGCTGAACTGGTGGTACACTAGAAGCACT[A/C]
TGTTGGTTGCTTGTGACCAAAGGCCTGCAGTTCGGGAAAACACCCCCTGGTAAATAGACTGGCCCCGTAGTTTGATGCTCAGCTATTGTGCCATCGACCA

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	37.30%	19.00%	2.69%	40.99%	NA
All Indica	2759	13.70%	23.30%	3.84%	59.22%	NA
All Japonica	1512	82.30%	4.60%	0.66%	12.50%	NA
Aus	269	4.10%	62.10%	2.97%	30.86%	NA
Indica I	595	23.40%	37.80%	0.67%	38.15%	NA
Indica II	465	16.60%	8.20%	6.45%	68.82%	NA
Indica III	913	3.20%	26.20%	4.05%	66.59%	NA
Indica Intermediate	786	16.80%	17.80%	4.45%	60.94%	NA
Temperate Japonica	767	97.90%	0.90%	0.00%	1.17%	NA
Tropical Japonica	504	57.90%	8.50%	1.98%	31.55%	NA
Japonica Intermediate	241	83.40%	7.90%	0.00%	8.71%	NA
VI/Aromatic	96	89.60%	1.00%	1.04%	8.33%	NA
Intermediate	90	52.20%	20.00%	2.22%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817490978	T -> G	LOC_Os08g28630.1	missense_variant ; p.His124Gln; MODERATE	stop_gained	Average:10.335; most accessible tissue: Callus, score: 50.422	N	N	N	N
vg0817490978	T -> G	LOC_Os08g28630.1	missense_variant ; p.His124Gln; MODERATE	nonsynonymous_codon ; H124Q	Average:10.335; most accessible tissue: Callus, score: 50.422	unknown	unknown	TOLERATED	0.64
vg0817490978	T -> DEL	LOC_Os08g28630.1	N	frameshift_variant	Average:10.335; most accessible tissue: Callus, score: 50.422	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817490978	NA	1.03E-06	mr1028	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
vg0817490978	NA	4.73E-06	mr1041	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
vg0817490978	NA	3.74E-11	mr1128	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
vg0817490978	NA	3.32E-06	mr1215	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
vg0817490978	NA	1.54E-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
vg0817490978	NA	5.75E-07	mr1369	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
vg0817490978	NA	2.70E-06	mr1445	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
vg0817490978	NA	6.63E-06	mr1511	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
vg0817490978	NA	4.74E-07	mr1824	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
vg0817490978	2.12E-06	NA	mr1963	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
vg0817490978	9.41E-07	NA	mr1963	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