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Detailed information for vg0618969985:

Variant ID: vg0618969985 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 18969985
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

CAGATGGTCATAAGGCTTGAGGCCCGATAGTTGGGCCGTGCCTGGGCCGATGCCTTGGCACGGTGGGCTGGCCCGACACGGCACAATCAAAGAAAAAGTT[G/A]
AGGAATCCAAAATAGACTTAACTCAGCCATACAAGACATGGCCCATAGAGAAGAAGGATACACGATAGACTTATTCCAACCATATAAAACATAGCCCAAA

Reverse complement sequence

TTTGGGCTATGTTTTATATGGTTGGAATAAGTCTATCGTGTATCCTTCTTCTCTATGGGCCATGTCTTGTATGGCTGAGTTAAGTCTATTTTGGATTCCT[C/T]
AACTTTTTCTTTGATTGTGCCGTGTCGGGCCAGCCCACCGTGCCAAGGCATCGGCCCAGGCACGGCCCAACTATCGGGCCTCAAGCCTTATGACCATCTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.60%	40.40%	0.55%	8.53%	NA
All Indica	2759	80.00%	19.00%	0.43%	0.62%	NA
All Japonica	1512	2.60%	77.60%	0.66%	19.05%	NA
Aus	269	37.20%	62.80%	0.00%	0.00%	NA
Indica I	595	79.50%	18.30%	0.34%	1.85%	NA
Indica II	465	93.30%	6.00%	0.43%	0.22%	NA
Indica III	913	78.00%	21.60%	0.22%	0.22%	NA
Indica Intermediate	786	74.80%	24.00%	0.76%	0.38%	NA
Temperate Japonica	767	3.70%	66.50%	1.30%	28.55%	NA
Tropical Japonica	504	0.80%	95.80%	0.00%	3.37%	NA
Japonica Intermediate	241	3.30%	75.10%	0.00%	21.58%	NA
VI/Aromatic	96	4.20%	6.20%	0.00%	89.58%	NA
Intermediate	90	42.20%	40.00%	4.44%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0618969985	G -> A	LOC_Os06g32610-LOC_Os06g32630	intergenic_region ; MODIFIER	silent_mutation	Average:75.277; most accessible tissue: Callus, score: 92.059	N	N	N	N
vg0618969985	G -> DEL	N	N	silent_mutation	Average:75.277; most accessible tissue: Callus, score: 92.059	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0618969985	NA	3.64E-34	mr1129	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
vg0618969985	NA	5.24E-14	mr1138	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
vg0618969985	NA	9.34E-06	mr1155	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
vg0618969985	NA	1.33E-30	mr1257	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
vg0618969985	NA	3.16E-10	mr1354	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
vg0618969985	NA	1.08E-06	mr1408	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
vg0618969985	9.22E-07	9.22E-07	mr1542	Jap_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
vg0618969985	NA	1.41E-09	mr1578	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
vg0618969985	NA	2.14E-10	mr1637	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
vg0618969985	NA	1.63E-08	mr1770	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
vg0618969985	9.88E-06	9.87E-06	mr1973	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
vg0618969985	NA	2.26E-06	mr1094_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
vg0618969985	NA	3.98E-12	mr1138_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
vg0618969985	NA	1.03E-07	mr1155_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
vg0618969985	NA	1.80E-09	mr1172_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
vg0618969985	NA	5.00E-06	mr1291_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
vg0618969985	NA	3.45E-07	mr1302_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
vg0618969985	NA	8.24E-10	mr1354_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
vg0618969985	NA	1.36E-06	mr1380_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
vg0618969985	NA	2.13E-06	mr1561_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
vg0618969985	NA	7.46E-07	mr1996_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