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Detailed information for vg0806359109:

Variant ID: vg0806359109 (JBrowse)	Variation Type: INDEL
Chromosome: chr08	Position: 6359109
Reference Allele: A	Alternative Allele: C,ACTTCC
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: 213. )

Flanking Sequence (100 bp) in Reference Genome:

CGCCGTCGATGCTTCCTGGACCTCTCCGACCCCTTTCAGCTGCACGGTGAGACACTGCATACCCCTGAACACCCCATGCATGCACCCATATAGCCCATTC[A/C,ACTTCC]
GAGCTGTAGCTCGACACGCATGCACATACCAAGAACCACCGCCGCTGTAGCTTGTTTTTCGCGAGCTACAGACCACCGCTGTAGCTGTAGCTTGTTCATC

Reverse complement sequence

GATGAACAAGCTACAGCTACAGCGGTGGTCTGTAGCTCGCGAAAAACAAGCTACAGCGGCGGTGGTTCTTGGTATGTGCATGCGTGTCGAGCTACAGCTC[T/G,GGAAGT]
GAATGGGCTATATGGGTGCATGCATGGGGTGTTCAGGGGTATGCAGTGTCTCACCGTGCAGCTGAAAGGGGTCGGAGAGGTCCAGGAAGCATCGACGGCG

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	78.10%	5.10%	3.51%	10.52%	ACTTCC: 2.77%
All Indica	2759	67.70%	7.50%	5.04%	15.55%	ACTTCC: 4.24%
All Japonica	1512	99.00%	0.10%	0.26%	0.66%	NA
Aus	269	72.50%	0.40%	7.06%	14.87%	ACTTCC: 5.20%
Indica I	595	66.90%	16.50%	2.86%	8.74%	ACTTCC: 5.04%
Indica II	465	63.00%	1.90%	3.23%	27.10%	ACTTCC: 4.73%
Indica III	913	67.70%	6.00%	7.89%	15.99%	ACTTCC: 2.41%
Indica Intermediate	786	71.10%	5.60%	4.45%	13.36%	ACTTCC: 5.47%
Temperate Japonica	767	99.50%	0.00%	0.13%	0.39%	NA
Tropical Japonica	504	98.20%	0.00%	0.60%	1.19%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	51.00%	32.30%	1.04%	15.62%	NA
Intermediate	90	90.00%	3.30%	3.33%	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
vg0806359109	A -> C	LOC_Os08g10790.1	downstream_gene_variant ; 2944.0bp to feature; MODIFIER	silent_mutation	Average:18.007; most accessible tissue: Callus, score: 43.373	N	N	N	N
vg0806359109	A -> C	LOC_Os08g10800.1	intron_variant ; MODIFIER	silent_mutation	Average:18.007; most accessible tissue: Callus, score: 43.373	N	N	N	N
vg0806359109	A -> DEL	N	N	silent_mutation	Average:18.007; most accessible tissue: Callus, score: 43.373	N	N	N	N
vg0806359109	A -> ACTTCC	LOC_Os08g10790.1	downstream_gene_variant ; 2945.0bp to feature; MODIFIER	silent_mutation	Average:18.007; most accessible tissue: Callus, score: 43.373	N	N	N	N
vg0806359109	A -> ACTTCC	LOC_Os08g10800.1	intron_variant ; MODIFIER	silent_mutation	Average:18.007; 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
vg0806359109	9.95E-08	2.73E-11	mr1038	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
vg0806359109	2.26E-09	2.81E-13	mr1038	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
vg0806359109	5.45E-08	4.34E-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
vg0806359109	2.47E-09	9.89E-13	mr1389	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
vg0806359109	6.20E-08	2.14E-13	mr1038_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
vg0806359109	1.99E-09	4.72E-14	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
vg0806359109	NA	1.28E-06	mr1057_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
vg0806359109	1.23E-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
vg0806359109	7.20E-07	NA	mr1141_2	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
vg0806359109	NA	5.88E-06	mr1220_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
vg0806359109	NA	3.15E-06	mr1266_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
vg0806359109	NA	2.55E-07	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
vg0806359109	NA	1.70E-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
vg0806359109	7.54E-07	7.53E-07	mr1906_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
vg0806359109	NA	1.19E-07	mr1909_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
vg0806359109	NA	3.85E-06	mr1924_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
vg0806359109	NA	5.35E-06	mr1951_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
vg0806359109	NA	5.89E-06	mr1960_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