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Detailed information for vg0504496687:

Variant ID: vg0504496687 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 4496687
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

TAAATTTGAAATGTGCTTCATCTGGATTTGTTATTTGTTGATACATTTTATGGTTGAAGAAGTGATGAAGGTGGTAAATTATTTGGCAGGTTCACTGTGC[C/T]
GTGTACAGTGGAAGGTGTTGGTAGCAGAACAAATATGCTGTATGATGTTGTTGTTTGTCTAAGTTTGAGCTGAATTTACGTTGTATGCCGTGTGCATAAT

Reverse complement sequence

ATTATGCACACGGCATACAACGTAAATTCAGCTCAAACTTAGACAAACAACAACATCATACAGCATATTTGTTCTGCTACCAACACCTTCCACTGTACAC[G/A]
GCACAGTGAACCTGCCAAATAATTTACCACCTTCATCACTTCTTCAACCATAAAATGTATCAACAAATAACAAATCCAGATGAAGCACATTTCAAATTTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.00%	15.90%	11.89%	7.19%	NA
All Indica	2759	42.70%	26.60%	19.57%	11.09%	NA
All Japonica	1512	97.90%	0.00%	0.40%	1.72%	NA
Aus	269	97.00%	1.10%	1.12%	0.74%	NA
Indica I	595	33.60%	23.40%	21.18%	21.85%	NA
Indica II	465	24.50%	43.00%	24.73%	7.74%	NA
Indica III	913	60.50%	17.10%	16.21%	6.24%	NA
Indica Intermediate	786	39.70%	30.50%	19.21%	10.56%	NA
Temperate Japonica	767	98.70%	0.00%	0.26%	1.04%	NA
Tropical Japonica	504	95.60%	0.00%	0.79%	3.57%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	4.20%	5.21%	0.00%	NA
Intermediate	90	74.40%	10.00%	8.89%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0504496687	C -> T	LOC_Os05g08250.1	upstream_gene_variant ; 4347.0bp to feature; MODIFIER	silent_mutation	Average:7.161; most accessible tissue: Callus, score: 21.163	N	N	N	N
vg0504496687	C -> T	LOC_Os05g08240.1	intron_variant ; MODIFIER	silent_mutation	Average:7.161; most accessible tissue: Callus, score: 21.163	N	N	N	N
vg0504496687	C -> DEL	N	N	silent_mutation	Average:7.161; most accessible tissue: Callus, score: 21.163	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0504496687	NA	5.58E-07	mr1157	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
vg0504496687	NA	3.05E-07	mr1328	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
vg0504496687	NA	2.54E-06	mr1328	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
vg0504496687	NA	1.37E-08	mr1446	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
vg0504496687	NA	4.46E-08	mr1989	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
vg0504496687	NA	9.62E-07	mr1090_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
vg0504496687	NA	3.14E-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
vg0504496687	NA	1.21E-07	mr1184_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
vg0504496687	NA	3.58E-07	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
vg0504496687	NA	5.45E-07	mr1278_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
vg0504496687	NA	8.76E-08	mr1329_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
vg0504496687	NA	8.54E-07	mr1337_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
vg0504496687	NA	3.06E-07	mr1488_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
vg0504496687	NA	3.25E-06	mr1492_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
vg0504496687	NA	7.98E-08	mr1508_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
vg0504496687	4.83E-07	1.58E-07	mr1508_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
vg0504496687	NA	2.16E-07	mr1524_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
vg0504496687	NA	6.97E-07	mr1754_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
vg0504496687	NA	1.70E-07	mr1779_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
vg0504496687	NA	3.34E-06	mr1982_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
vg0504496687	NA	4.30E-06	mr1992_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