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Detailed information for vg0502700156:

Variant ID: vg0502700156 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 2700156
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: 232. )

Flanking Sequence (100 bp) in Reference Genome:

AATAGACTTACTCCTTATAAAATTGTTGGCTTTCAGGCTAAGGTCGTGTTTAGTTTCAAAATATTTTCTTCAAACTTACAACTTTTTCGTCACATCAAAT[G/A]
TTTAGACACATGCATGGAGTATTAAATGTGGACGAAAAAAACCAATTGCACAGTTTGCATGTAAATCACGAGACAAATATTTTGAGCCTAATTATGCCAT

Reverse complement sequence

ATGGCATAATTAGGCTCAAAATATTTGTCTCGTGATTTACATGCAAACTGTGCAATTGGTTTTTTTCGTCCACATTTAATACTCCATGCATGTGTCTAAA[C/T]
ATTTGATGTGACGAAAAAGTTGTAAGTTTGAAGAAAATATTTTGAAACTAAACACGACCTTAGCCTGAAAGCCAACAATTTTATAAGGAGTAAGTCTATT

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	71.60%	27.80%	0.30%	0.32%	NA
All Indica	2759	55.00%	44.00%	0.47%	0.54%	NA
All Japonica	1512	98.90%	1.10%	0.00%	0.00%	NA
Aus	269	77.00%	23.00%	0.00%	0.00%	NA
Indica I	595	55.60%	43.50%	0.50%	0.34%	NA
Indica II	465	46.20%	52.30%	0.43%	1.08%	NA
Indica III	913	56.20%	43.40%	0.11%	0.33%	NA
Indica Intermediate	786	58.40%	40.10%	0.89%	0.64%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	1.11%	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
vg0502700156	G -> DEL	N	N	silent_mutation	Average:49.966; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg0502700156	G -> A	LOC_Os05g05420.1	upstream_gene_variant ; 3758.0bp to feature; MODIFIER	silent_mutation	Average:49.966; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg0502700156	G -> A	LOC_Os05g05430.1	upstream_gene_variant ; 377.0bp to feature; MODIFIER	silent_mutation	Average:49.966; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg0502700156	G -> A	LOC_Os05g05440.1	downstream_gene_variant ; 3239.0bp to feature; MODIFIER	silent_mutation	Average:49.966; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg0502700156	G -> A	LOC_Os05g05430-LOC_Os05g05440	intergenic_region ; MODIFIER	silent_mutation	Average:49.966; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0502700156	NA	6.37E-09	mr1624_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
vg0502700156	NA	1.98E-07	mr1925_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
vg0502700156	7.22E-06	NA	mr1944_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
vg0502700156	2.59E-06	4.13E-06	mr1944_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
vg0502700156	5.56E-06	2.14E-06	mr1954_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