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Detailed information for vg0406038870:

Variant ID: vg0406038870 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6038870
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

AGTGGTTTCGCTCGGAGTCCCCACGGTCGGCGCCAGCTGTTGTCGAAACGACAACTGCATACGTCGGAGGACGTGGTTACTCAACAGTGGTTGGGAAAAT[G/A]
AAGTGTACTAAATTTTTAATTTTTCTTGGATCCCCCCATTACATGGCCCTAGGGGACTATTTATAGCCCCATTACAGGTCCTTACTACCAGCGTTTAGGT

Reverse complement sequence

ACCTAAACGCTGGTAGTAAGGACCTGTAATGGGGCTATAAATAGTCCCCTAGGGCCATGTAATGGGGGGATCCAAGAAAAATTAAAAATTTAGTACACTT[C/T]
ATTTTCCCAACCACTGTTGAGTAACCACGTCCTCCGACGTATGCAGTTGTCGTTTCGACAACAGCTGGCGCCGACCGTGGGGACTCCGAGCGAAACCACT

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	78.20%	7.60%	5.27%	8.93%	NA
All Indica	2759	66.60%	11.00%	8.77%	13.66%	NA
All Japonica	1512	96.90%	0.50%	0.33%	2.25%	NA
Aus	269	97.40%	0.40%	0.37%	1.86%	NA
Indica I	595	72.40%	5.40%	10.76%	11.43%	NA
Indica II	465	63.20%	6.00%	16.13%	14.62%	NA
Indica III	913	64.00%	16.40%	6.02%	13.58%	NA
Indica Intermediate	786	67.20%	11.80%	6.11%	14.89%	NA
Temperate Japonica	767	99.50%	0.10%	0.13%	0.26%	NA
Tropical Japonica	504	95.00%	0.80%	0.60%	3.57%	NA
Japonica Intermediate	241	92.50%	1.20%	0.41%	5.81%	NA
VI/Aromatic	96	58.30%	40.60%	0.00%	1.04%	NA
Intermediate	90	82.20%	11.10%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406038870	G -> DEL	N	N	silent_mutation	Average:46.482; most accessible tissue: Minghui63 flag leaf, score: 72.907	N	N	N	N
vg0406038870	G -> A	LOC_Os04g11090.1	upstream_gene_variant ; 499.0bp to feature; MODIFIER	silent_mutation	Average:46.482; most accessible tissue: Minghui63 flag leaf, score: 72.907	N	N	N	N
vg0406038870	G -> A	LOC_Os04g11100.1	upstream_gene_variant ; 2583.0bp to feature; MODIFIER	silent_mutation	Average:46.482; most accessible tissue: Minghui63 flag leaf, score: 72.907	N	N	N	N
vg0406038870	G -> A	LOC_Os04g11090-LOC_Os04g11100	intergenic_region ; MODIFIER	silent_mutation	Average:46.482; most accessible tissue: Minghui63 flag leaf, score: 72.907	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406038870	NA	5.41E-06	mr1043	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
vg0406038870	NA	2.67E-07	mr1088	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
vg0406038870	NA	2.27E-06	mr1104	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
vg0406038870	7.78E-07	7.58E-08	mr1210	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
vg0406038870	NA	3.04E-09	mr1213	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
vg0406038870	NA	6.14E-09	mr1246	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
vg0406038870	1.66E-07	9.78E-10	mr1305	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
vg0406038870	NA	6.61E-06	mr1409	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
vg0406038870	NA	3.18E-06	mr1502	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
vg0406038870	NA	3.95E-06	mr1515	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
vg0406038870	NA	4.31E-06	mr1552	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
vg0406038870	3.03E-06	1.67E-09	mr1586	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
vg0406038870	NA	8.98E-07	mr1620	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
vg0406038870	2.11E-06	1.76E-06	mr1765	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
vg0406038870	NA	4.72E-07	mr1798	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
vg0406038870	NA	4.54E-06	mr1846	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