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Detailed information for vg0806359100:

Variant ID: vg0806359100 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 6359100
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CATCTCCAACGCCGTCGATGCTTCCTGGACCTCTCCGACCCCTTTCAGCTGCACGGTGAGACACTGCATACCCCTGAACACCCCATGCATGCACCCATAT[A/C]
GCCCATTCAGAGCTGTAGCTCGACACGCATGCACATACCAAGAACCACCGCCGCTGTAGCTTGTTTTTCGCGAGCTACAGACCACCGCTGTAGCTGTAGC

Reverse complement sequence

GCTACAGCTACAGCGGTGGTCTGTAGCTCGCGAAAAACAAGCTACAGCGGCGGTGGTTCTTGGTATGTGCATGCGTGTCGAGCTACAGCTCTGAATGGGC[T/G]
ATATGGGTGCATGCATGGGGTGTTCAGGGGTATGCAGTGTCTCACCGTGCAGCTGAAAGGGGTCGGAGAGGTCCAGGAAGCATCGACGGCGTTGGAGATG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.00%	2.90%	1.59%	7.51%	NA
All Indica	2759	80.60%	5.00%	2.43%	11.96%	NA
All Japonica	1512	99.30%	0.00%	0.13%	0.60%	NA
Aus	269	98.10%	0.00%	1.86%	0.00%	NA
Indica I	595	79.50%	13.10%	3.03%	4.37%	NA
Indica II	465	71.00%	1.10%	1.94%	26.02%	NA
Indica III	913	82.80%	3.00%	2.08%	12.16%	NA
Indica Intermediate	786	84.60%	3.60%	2.67%	9.16%	NA
Temperate Japonica	767	99.50%	0.00%	0.13%	0.39%	NA
Tropical Japonica	504	98.80%	0.00%	0.20%	0.99%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	85.40%	0.00%	1.04%	13.54%	NA
Intermediate	90	96.70%	0.00%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0806359100	A -> C	LOC_Os08g10790.1	downstream_gene_variant ; 2935.0bp to feature; MODIFIER	silent_mutation	Average:15.757; most accessible tissue: Callus, score: 43.373	N	N	N	N
vg0806359100	A -> C	LOC_Os08g10800.1	intron_variant ; MODIFIER	silent_mutation	Average:15.757; most accessible tissue: Callus, score: 43.373	N	N	N	N
vg0806359100	A -> DEL	N	N	silent_mutation	Average:15.757; most accessible tissue: Callus, score: 43.373	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0806359100	3.80E-08	1.09E-11	mr1038	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
vg0806359100	4.94E-08	1.37E-11	mr1038	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
vg0806359100	9.28E-08	7.51E-12	mr1389	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
vg0806359100	1.40E-07	6.82E-11	mr1389	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
vg0806359100	6.67E-09	7.85E-14	mr1038_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
vg0806359100	2.72E-08	1.84E-12	mr1038_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
vg0806359100	4.57E-06	NA	mr1141_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
vg0806359100	5.43E-06	NA	mr1141_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
vg0806359100	2.16E-06	1.66E-09	mr1389_2	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
vg0806359100	3.23E-06	3.54E-09	mr1389_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