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Detailed information for vg0818608910:

Variant ID: vg0818608910 (JBrowse)	Variation Type: INDEL
Chromosome: chr08	Position: 18608910
Reference Allele: G	Alternative Allele: GAATGATGAGAACAAGCGAAGTGGAAAAACGA,A
Primary Allele: G	Secondary Allele: GAATGATGAGAACAAGCGAA GTGGAAAAACGA

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCCCTCCTCCTGTGTTTGCATCTCTCCCCTCTACAACAAATTGCTCTCCCTATATCTCCATCTTCATAGCTTGGATCAACAAGCGAAGTGGAAAAACG[G/GAATGATGAGAACAAGCGAAGTGGAAAAACGA,A]
AATGATGAGGAGGAGAGGAGTAGGAGGGGTTAGATCGGAGTCTCCCCTATTGTCTCCTCACAAGTTCTCTAAAAAAACCCTAGGTGATGAGGACATCCCA

Reverse complement sequence

TGGGATGTCCTCATCACCTAGGGTTTTTTTAGAGAACTTGTGAGGAGACAATAGGGGAGACTCCGATCTAACCCCTCCTACTCCTCTCCTCCTCATCATT[C/TCGTTTTTCCACTTCGCTTGTTCTCATCATTC,T]
CGTTTTTCCACTTCGCTTGTTGATCCAAGCTATGAAGATGGAGATATAGGGAGAGCAATTTGTTGTAGAGGGGAGAGATGCAAACACAGGAGGAGGGGAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of GAATGATGAGAACAAGCGAA GTGGAAAAACGA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.20%	13.70%	0.04%	0.00%	A: 0.11%
All Indica	2759	76.50%	23.20%	0.07%	0.00%	A: 0.18%
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	67.70%	31.80%	0.00%	0.00%	A: 0.50%
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	65.00%	34.90%	0.11%	0.00%	NA
Indica Intermediate	786	83.30%	16.30%	0.13%	0.00%	A: 0.25%
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818608910	G -> A	LOC_Os08g30260-LOC_Os08g30270	intergenic_region ; MODIFIER	silent_mutation	Average:51.951; most accessible tissue: Zhenshan97 young leaf, score: 73.54	N	N	N	N
vg0818608910	G -> GAATGATGAGAACAAGCGAAGTGGAAAAAC GA	LOC_Os08g30260-LOC_Os08g30270	intergenic_region ; MODIFIER	silent_mutation	Average:51.951; most accessible tissue: Zhenshan97 young leaf, score: 73.54	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818608910	NA	1.15E-06	mr1096	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
vg0818608910	4.84E-07	NA	mr1486	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
vg0818608910	6.29E-08	1.74E-06	mr1486	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
vg0818608910	3.25E-07	NA	mr1548	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
vg0818608910	2.14E-07	8.16E-07	mr1548	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
vg0818608910	4.63E-06	NA	mr1588	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
vg0818608910	4.63E-06	3.32E-06	mr1588	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
vg0818608910	2.95E-06	NA	mr1486_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
vg0818608910	1.06E-07	NA	mr1588_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
vg0818608910	2.42E-08	2.46E-06	mr1588_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