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Detailed information for vg0811929425:

Variant ID: vg0811929425 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 11929425
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: 42. )

Flanking Sequence (100 bp) in Reference Genome:

ATCGGCACTTAGCCGATCGGCTATCGTTTATGGATTCAACCGCAGTTTCTTTGTCTTTGTTCTTGTTGATTGCAGGATCAAATCAACTGGCACGCTAGCA[C/T]
ACCCGAAGGTGAGTTTTGGACCTACACTGGAGTTAAGCAGATCTCCCAGGCCTTGTGTTTTCACATCAACACGCTTTTGGCACGCCCGGTGGGACCGATC

Reverse complement sequence

GATCGGTCCCACCGGGCGTGCCAAAAGCGTGTTGATGTGAAAACACAAGGCCTGGGAGATCTGCTTAACTCCAGTGTAGGTCCAAAACTCACCTTCGGGT[G/A]
TGCTAGCGTGCCAGTTGATTTGATCCTGCAATCAACAAGAACAAAGACAAAGAAACTGCGGTTGAATCCATAAACGATAGCCGATCGGCTAAGTGCCGAT

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	27.40%	7.60%	9.67%	55.27%	NA
All Indica	2759	11.90%	12.60%	14.10%	61.33%	NA
All Japonica	1512	61.40%	0.30%	2.18%	36.04%	NA
Aus	269	1.10%	0.70%	6.69%	91.45%	NA
Indica I	595	3.90%	9.40%	11.60%	75.13%	NA
Indica II	465	10.50%	10.50%	12.04%	66.88%	NA
Indica III	913	18.00%	17.60%	13.91%	50.49%	NA
Indica Intermediate	786	11.80%	10.60%	17.43%	60.18%	NA
Temperate Japonica	767	85.40%	0.40%	2.61%	11.60%	NA
Tropical Japonica	504	36.50%	0.20%	1.98%	61.31%	NA
Japonica Intermediate	241	37.30%	0.40%	1.24%	61.00%	NA
VI/Aromatic	96	7.30%	0.00%	5.21%	87.50%	NA
Intermediate	90	31.10%	5.60%	13.33%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0811929425	C -> T	LOC_Os08g19920.1	missense_variant ; p.His75Tyr; MODERATE	nonsynonymous_codon ; H75Y	Average:17.1; most accessible tissue: Callus, score: 41.048	unknown	unknown	TOLERATED	1.00
vg0811929425	C -> DEL	LOC_Os08g19920.1	N	frameshift_variant	Average:17.1; most accessible tissue: Callus, score: 41.048	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0811929425	NA	3.62E-06	mr1044	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
vg0811929425	NA	3.84E-06	mr1049	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
vg0811929425	NA	5.13E-08	mr1238	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
vg0811929425	NA	1.88E-07	mr1309	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
vg0811929425	NA	6.12E-06	mr1318	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
vg0811929425	NA	1.33E-06	mr1704	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
vg0811929425	8.61E-08	5.95E-11	mr1708	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
vg0811929425	NA	3.91E-07	mr1708	Jap_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
vg0811929425	NA	8.11E-06	mr1794	Jap_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
vg0811929425	NA	4.77E-07	mr1803	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
vg0811929425	NA	3.47E-08	mr1841	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
vg0811929425	NA	1.90E-09	mr1864	Jap_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
vg0811929425	2.83E-08	2.83E-08	mr1900	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
vg0811929425	NA	3.91E-06	mr1011_2	Jap_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
vg0811929425	NA	7.71E-06	mr1170_2	Jap_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
vg0811929425	NA	1.82E-06	mr1509_2	Jap_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
vg0811929425	NA	8.56E-06	mr1900_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