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Detailed information for vg0613339384:

Variant ID: vg0613339384 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13339384
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

TGGGGCCCATTCATCAAAAAGCGACGGGGCATTCCATACCTAACCTCTGTGAGGGTCCACTTGTAAAAAATGGTTACTATTTAATCCTCCATGACTATAA[G/A]
GGGATTAGTGGAGGATCAATCCACTAAAGAGAGGATCTGGATAGAACGTAGAATTTAGTTAAGGAAATCTAGCCCTTGTAGCCAATTGATTCGACCACAT

Reverse complement sequence

ATGTGGTCGAATCAATTGGCTACAAGGGCTAGATTTCCTTAACTAAATTCTACGTTCTATCCAGATCCTCTCTTTAGTGGATTGATCCTCCACTAATCCC[C/T]
TTATAGTCATGGAGGATTAAATAGTAACCATTTTTTACAAGTGGACCCTCACAGAGGTTAGGTATGGAATGCCCCGTCGCTTTTTGATGAATGGGCCCCA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.10%	9.40%	1.42%	0.00%	NA
All Indica	2759	82.30%	15.30%	2.39%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	94.80%	0.50%	4.71%	0.00%	NA
Indica II	465	85.80%	12.00%	2.15%	0.00%	NA
Indica III	913	69.10%	30.20%	0.66%	0.00%	NA
Indica Intermediate	786	86.10%	11.10%	2.80%	0.00%	NA
Temperate Japonica	767	98.60%	1.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0613339384	G -> A	LOC_Os06g22860.1	downstream_gene_variant ; 2029.0bp to feature; MODIFIER	silent_mutation	Average:55.265; most accessible tissue: Zhenshan97 young leaf, score: 73.54	N	N	N	N
vg0613339384	G -> A	LOC_Os06g22860-LOC_Os06g22870	intergenic_region ; MODIFIER	silent_mutation	Average:55.265; 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
vg0613339384	6.38E-06	NA	mr1068	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
vg0613339384	5.11E-07	NA	mr1096	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
vg0613339384	6.29E-07	NA	mr1111	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
vg0613339384	7.70E-07	NA	mr1121	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
vg0613339384	3.07E-07	NA	mr1144	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
vg0613339384	7.20E-06	NA	mr1144	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
vg0613339384	3.66E-06	NA	mr1068_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
vg0613339384	3.24E-06	NA	mr1068_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
vg0613339384	1.01E-06	NA	mr1111_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
vg0613339384	2.89E-06	NA	mr1111_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
vg0613339384	3.28E-07	NA	mr1121_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
vg0613339384	2.69E-06	4.32E-06	mr1121_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
vg0613339384	3.46E-06	NA	mr1144_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
vg0613339384	9.94E-06	NA	mr1144_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
vg0613339384	5.71E-06	NA	mr1211_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