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Detailed information for vg0602363435:

Variant ID: vg0602363435 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 2363435
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: 304. )

Flanking Sequence (100 bp) in Reference Genome:

AACTAATGGCTCCAATTAGTATGTGTTTTTTTTTCCCTAGCATGTCACACTGCTGGTACCAGGACACTGATTTCTCCTTTAAAGAACTTTTGTGGTGGTG[G/A]
TTGTGGGGAACCACTTGTACAGTTCTGCTATAGCTTATCTTTCAGTTGCAATATGGGGATAAGTCCTAAAGAATTAAGAAAGAAATGGCTATAGCCCCAC

Reverse complement sequence

GTGGGGCTATAGCCATTTCTTTCTTAATTCTTTAGGACTTATCCCCATATTGCAACTGAAAGATAAGCTATAGCAGAACTGTACAAGTGGTTCCCCACAA[C/T]
CACCACCACAAAAGTTCTTTAAAGGAGAAATCAGTGTCCTGGTACCAGCAGTGTGACATGCTAGGGAAAAAAAAACACATACTAATTGGAGCCATTAGTT

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	96.30%	3.40%	0.28%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	90.10%	9.30%	0.66%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.30%	0.13%	0.00%	NA
Tropical Japonica	504	72.00%	26.40%	1.59%	0.00%	NA
Japonica Intermediate	241	97.50%	2.10%	0.41%	0.00%	NA
VI/Aromatic	96	86.50%	12.50%	1.04%	0.00%	NA
Intermediate	90	94.40%	3.30%	2.22%	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
vg0602363435	G -> A	LOC_Os06g05250.1	downstream_gene_variant ; 3167.0bp to feature; MODIFIER	silent_mutation	Average:54.772; most accessible tissue: Callus, score: 76.31	N	N	N	N
vg0602363435	G -> A	LOC_Os06g05250.2	downstream_gene_variant ; 3634.0bp to feature; MODIFIER	silent_mutation	Average:54.772; most accessible tissue: Callus, score: 76.31	N	N	N	N
vg0602363435	G -> A	LOC_Os06g05240.1	intron_variant ; MODIFIER	silent_mutation	Average:54.772; most accessible tissue: Callus, score: 76.31	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0602363435	NA	6.98E-06	mr1076	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
vg0602363435	NA	6.64E-07	mr1082	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
vg0602363435	8.14E-06	4.62E-09	mr1083	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
vg0602363435	5.79E-08	5.79E-08	mr1204	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
vg0602363435	NA	3.21E-07	mr1226	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
vg0602363435	NA	7.25E-06	mr1227	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
vg0602363435	NA	1.69E-06	mr1411	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
vg0602363435	NA	4.99E-06	mr1560	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
vg0602363435	NA	5.41E-06	mr1878	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
vg0602363435	NA	6.22E-06	mr1949	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
vg0602363435	2.07E-06	2.07E-06	mr1076_2	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
vg0602363435	NA	7.80E-06	mr1104_2	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
vg0602363435	NA	2.58E-08	mr1226_2	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