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Detailed information for vg0331916551:

Variant ID: vg0331916551 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 31916551
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

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

Flanking Sequence (100 bp) in Reference Genome:

CTAATTTATGTGTAATTTAGCTTTAATTTTGGTTGAATATGAAGCATATGCATGGCAATTATTTTGAGGTAGAGGACCTAATGAAACTATGGTGAAAGTC[C/G]
GTACATGTGCATACTCCTACTAAGTATATAATAATAAGATATATGATACAGTATTATTTTACAATTGAGAGATTAGGAAGAAATGGTTAGATTGAGTCAA

Reverse complement sequence

TTGACTCAATCTAACCATTTCTTCCTAATCTCTCAATTGTAAAATAATACTGTATCATATATCTTATTATTATATACTTAGTAGGAGTATGCACATGTAC[G/C]
GACTTTCACCATAGTTTCATTAGGTCCTCTACCTCAAAATAATTGCCATGCATATGCTTCATATTCAACCAAAATTAAAGCTAAATTACACATAAATTAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.10%	8.60%	0.32%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	73.80%	25.30%	0.86%	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	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.50%	0.40%	0.13%	0.00%	NA
Tropical Japonica	504	25.20%	73.00%	1.79%	0.00%	NA
Japonica Intermediate	241	93.80%	5.00%	1.24%	0.00%	NA
VI/Aromatic	96	94.80%	4.20%	1.04%	0.00%	NA
Intermediate	90	83.30%	15.60%	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
vg0331916551	C -> G	LOC_Os03g56040.1	downstream_gene_variant ; 3650.0bp to feature; MODIFIER	silent_mutation	Average:60.995; most accessible tissue: Callus, score: 98.185	N	N	N	N
vg0331916551	C -> G	LOC_Os03g56040-LOC_Os03g56050	intergenic_region ; MODIFIER	silent_mutation	Average:60.995; most accessible tissue: Callus, score: 98.185	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0331916551	NA	2.98E-08	mr1551	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
vg0331916551	NA	3.76E-07	mr1554	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
vg0331916551	NA	6.82E-07	mr1696	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
vg0331916551	1.04E-08	NA	mr1745	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
vg0331916551	NA	1.58E-07	mr1090_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
vg0331916551	NA	6.88E-10	mr1398_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
vg0331916551	NA	1.29E-06	mr1398_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
vg0331916551	NA	2.15E-07	mr1551_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
vg0331916551	NA	3.97E-07	mr1623_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
vg0331916551	NA	5.08E-09	mr1696_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
vg0331916551	NA	2.03E-07	mr1696_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
vg0331916551	8.80E-08	NA	mr1745_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
vg0331916551	NA	2.32E-08	mr1905_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