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Detailed information for vg0109353965:

Variant ID: vg0109353965 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 9353965
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCTAAATTGAATTTTTAATTGGCCTCAAGAAAATATCGGTGTAAAAGCAAGAGAGAAACCCTAAATAAATTAATGCGAATAATAATCGGAATTGGCAT[A/G]
TGGAATTTTTCTTGAGTTCTACATGTCGAAATGTGCTAACAAGATTTTTAGTGGAATTTTCAGAGCTCTAGAAATAATTTTAACCAATTAAAATCGAGCA

Reverse complement sequence

TGCTCGATTTTAATTGGTTAAAATTATTTCTAGAGCTCTGAAAATTCCACTAAAAATCTTGTTAGCACATTTCGACATGTAGAACTCAAGAAAAATTCCA[T/C]
ATGCCAATTCCGATTATTATTCGCATTAATTTATTTAGGGTTTCTCTCTTGCTTTTACACCGATATTTTCTTGAGGCCAATTAAAAATTCAATTTAGGCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.00%	16.80%	8.55%	47.67%	NA
All Indica	2759	3.10%	23.70%	4.82%	68.43%	NA
All Japonica	1512	72.50%	1.30%	15.54%	10.65%	NA
Aus	269	0.70%	41.60%	3.35%	54.28%	NA
Indica I	595	3.40%	14.80%	4.03%	77.82%	NA
Indica II	465	3.00%	16.60%	2.58%	77.85%	NA
Indica III	913	2.00%	35.80%	7.67%	54.55%	NA
Indica Intermediate	786	4.20%	20.50%	3.44%	71.88%	NA
Temperate Japonica	767	67.00%	0.30%	15.38%	17.34%	NA
Tropical Japonica	504	82.30%	3.20%	11.51%	2.98%	NA
Japonica Intermediate	241	69.30%	0.80%	24.48%	5.39%	NA
VI/Aromatic	96	68.80%	0.00%	18.75%	12.50%	NA
Intermediate	90	31.10%	7.80%	10.00%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0109353965	A -> G	LOC_Os01g16470.1	downstream_gene_variant ; 2629.0bp to feature; MODIFIER	silent_mutation	Average:51.55; most accessible tissue: Zhenshan97 flag leaf, score: 65.3	N	N	N	N
vg0109353965	A -> G	LOC_Os01g16480.1	intron_variant ; MODIFIER	silent_mutation	Average:51.55; most accessible tissue: Zhenshan97 flag leaf, score: 65.3	N	N	N	N
vg0109353965	A -> DEL	N	N	silent_mutation	Average:51.55; most accessible tissue: Zhenshan97 flag leaf, score: 65.3	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0109353965	3.18E-06	NA	mr1301	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
vg0109353965	1.41E-06	1.41E-06	mr1347	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
vg0109353965	4.59E-06	NA	mr1382	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
vg0109353965	NA	2.24E-06	mr1382	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
vg0109353965	4.56E-06	3.62E-08	mr1398	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
vg0109353965	NA	2.96E-07	mr1398	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
vg0109353965	1.63E-09	NA	mr1422	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
vg0109353965	5.87E-06	3.40E-08	mr1422	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
vg0109353965	NA	1.11E-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
vg0109353965	NA	3.50E-06	mr1602	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
vg0109353965	8.46E-06	NA	mr1696	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
vg0109353965	NA	2.76E-07	mr1993	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
vg0109353965	NA	9.39E-08	mr1084_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
vg0109353965	NA	2.35E-06	mr1206_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
vg0109353965	NA	7.89E-06	mr1405_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
vg0109353965	NA	6.36E-06	mr1419_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
vg0109353965	NA	6.15E-08	mr1668_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