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Detailed information for vg0918924003:

Variant ID: vg0918924003 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 18924003
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGGAATAAGTAGCTTTTAGTGGCAAACTATCTGTTGGGAAAGATAAAGTGGCATAGTATAATTTTTTTCTACCGACAGACAATTGTCTTCTTTTTAGT[G/A]
TTGTAGTGTAGTGTGTGTGCGCGCGCATAAAACATACACATATAGTTCTAGCTCATGCATATGTATCTTTTGTTTGATGCATATGTTGGGTTCAATTCCA

Reverse complement sequence

TGGAATTGAACCCAACATATGCATCAAACAAAAGATACATATGCATGAGCTAGAACTATATGTGTATGTTTTATGCGCGCGCACACACACTACACTACAA[C/T]
ACTAAAAAGAAGACAATTGTCTGTCGGTAGAAAAAAATTATACTATGCCACTTTATCTTTCCCAACAGATAGTTTGCCACTAAAAGCTACTTATTCCAAC

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	61.20%	38.50%	0.28%	0.00%	NA
All Indica	2759	34.20%	65.30%	0.47%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	16.80%	83.00%	0.17%	0.00%	NA
Indica II	465	71.60%	27.50%	0.86%	0.00%	NA
Indica III	913	20.50%	78.90%	0.66%	0.00%	NA
Indica Intermediate	786	41.20%	58.50%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	0.00%	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
vg0918924003	G -> A	LOC_Os09g31438.1	upstream_gene_variant ; 2347.0bp to feature; MODIFIER	silent_mutation	Average:54.633; most accessible tissue: Callus, score: 80.742	N	N	N	N
vg0918924003	G -> A	LOC_Os09g31438-LOC_Os09g31442	intergenic_region ; MODIFIER	silent_mutation	Average:54.633; most accessible tissue: Callus, score: 80.742	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0918924003	9.58E-06	NA	mr1105	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
vg0918924003	2.52E-09	1.06E-14	mr1231	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
vg0918924003	3.81E-09	3.73E-13	mr1231	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
vg0918924003	8.80E-11	NA	mr1232	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
vg0918924003	1.14E-10	2.04E-11	mr1232	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
vg0918924003	8.59E-23	NA	mr1557	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
vg0918924003	1.06E-22	3.95E-33	mr1557	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
vg0918924003	9.34E-21	1.67E-46	mr1598	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
vg0918924003	7.46E-16	4.08E-23	mr1598	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
vg0918924003	NA	3.45E-08	mr1610	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
vg0918924003	6.55E-10	NA	mr1944	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
vg0918924003	3.00E-10	5.04E-14	mr1944	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
vg0918924003	NA	3.97E-09	mr1050_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
vg0918924003	NA	5.75E-08	mr1232_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
vg0918924003	NA	8.67E-06	mr1233_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
vg0918924003	NA	2.39E-06	mr1272_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
vg0918924003	NA	3.21E-19	mr1531_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
vg0918924003	NA	3.62E-07	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
vg0918924003	2.30E-15	NA	mr1557_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
vg0918924003	6.89E-15	6.23E-25	mr1557_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
vg0918924003	1.60E-18	3.60E-67	mr1598_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
vg0918924003	3.11E-15	7.52E-29	mr1598_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