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Detailed information for vg0507041473:

Variant ID: vg0507041473 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7041473
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

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

Flanking Sequence (100 bp) in Reference Genome:

ACAAAACCACACTATCAATAAATGGATTCACATGTGAGATGACGTAGTTGTTACACCTAGGATGAGAATATGGCATCCTATTAATTTCGTGTGATGGCTG[G/T]
TAATAAGATGCCACGTCCTCGTCATAAGTGGAACAGCCACGCCATATCACGGGTGAATCAATTCATTGATAGTGTGATTTTCTGAAACTACACTACTAAA

Reverse complement sequence

TTTAGTAGTGTAGTTTCAGAAAATCACACTATCAATGAATTGATTCACCCGTGATATGGCGTGGCTGTTCCACTTATGACGAGGACGTGGCATCTTATTA[C/A]
CAGCCATCACACGAAATTAATAGGATGCCATATTCTCATCCTAGGTGTAACAACTACGTCATCTCACATGTGAATCCATTTATTGATAGTGTGGTTTTGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.70%	29.80%	0.15%	0.42%	NA
All Indica	2759	51.20%	48.10%	0.22%	0.54%	NA
All Japonica	1512	99.50%	0.30%	0.07%	0.13%	NA
Aus	269	77.30%	22.70%	0.00%	0.00%	NA
Indica I	595	28.20%	71.80%	0.00%	0.00%	NA
Indica II	465	75.10%	24.30%	0.22%	0.43%	NA
Indica III	913	56.20%	42.80%	0.11%	0.88%	NA
Indica Intermediate	786	48.60%	50.30%	0.51%	0.64%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.60%	0.20%	0.00%	NA
Japonica Intermediate	241	98.80%	0.40%	0.00%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	80.00%	16.70%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0507041473	G -> T	LOC_Os05g12260.1	downstream_gene_variant ; 4719.0bp to feature; MODIFIER	silent_mutation	Average:45.69; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0507041473	G -> T	LOC_Os05g12270.1	downstream_gene_variant ; 1114.0bp to feature; MODIFIER	silent_mutation	Average:45.69; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0507041473	G -> T	LOC_Os05g12270-LOC_Os05g12280	intergenic_region ; MODIFIER	silent_mutation	Average:45.69; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0507041473	G -> DEL	N	N	silent_mutation	Average:45.69; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507041473	NA	5.24E-12	mr1195	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
vg0507041473	2.63E-10	1.11E-23	mr1531	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
vg0507041473	1.82E-10	1.75E-15	mr1531	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
vg0507041473	8.48E-21	1.17E-27	mr1593	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
vg0507041473	1.27E-16	2.22E-32	mr1593	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
vg0507041473	NA	2.70E-08	mr1860	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
vg0507041473	NA	5.72E-06	mr1904	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
vg0507041473	4.17E-10	8.33E-27	mr1195_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
vg0507041473	1.85E-08	2.54E-14	mr1195_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
vg0507041473	NA	3.27E-09	mr1531_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
vg0507041473	1.24E-23	5.50E-35	mr1593_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
vg0507041473	1.48E-18	5.54E-44	mr1593_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
vg0507041473	NA	8.46E-06	mr1961_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