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Detailed information for vg1103603106:

Variant ID: vg1103603106 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 3603106
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCCATGCAAGTTTTGGAGGAATTTTAACATGAGGTAAAACCTCTTGGAAACTTTCCTTTGAGTCTTTATCTCTCCTCTAATTCCTGCGTTTTTCCTGT[G/A]
GTCCAATCAAACGATCGTTCCTGTGTTTTTCCTGTGTTTTGCAATCCTCTGTTTTACACTTACATTCCTATCAAAATCCTGCGTTTTTTCTATTCCTATG

Reverse complement sequence

CATAGGAATAGAAAAAACGCAGGATTTTGATAGGAATGTAAGTGTAAAACAGAGGATTGCAAAACACAGGAAAAACACAGGAACGATCGTTTGATTGGAC[C/T]
ACAGGAAAAACGCAGGAATTAGAGGAGAGATAAAGACTCAAAGGAAAGTTTCCAAGAGGTTTTACCTCATGTTAAAATTCCTCCAAAACTTGCATGGCAT

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	45.10%	36.00%	1.23%	17.69%	NA
All Indica	2759	57.60%	12.90%	1.74%	27.80%	NA
All Japonica	1512	16.90%	80.60%	0.13%	2.45%	NA
Aus	269	69.50%	20.40%	2.97%	7.06%	NA
Indica I	595	33.30%	13.30%	4.03%	49.41%	NA
Indica II	465	83.20%	6.50%	0.65%	9.68%	NA
Indica III	913	64.10%	12.00%	1.20%	22.67%	NA
Indica Intermediate	786	53.20%	17.40%	1.27%	28.12%	NA
Temperate Japonica	767	2.60%	97.30%	0.13%	0.00%	NA
Tropical Japonica	504	41.30%	51.80%	0.20%	6.75%	NA
Japonica Intermediate	241	11.20%	87.60%	0.00%	1.24%	NA
VI/Aromatic	96	55.20%	43.80%	0.00%	1.04%	NA
Intermediate	90	55.60%	31.10%	0.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1103603106	G -> A	LOC_Os11g07200.1	upstream_gene_variant ; 3913.0bp to feature; MODIFIER	silent_mutation	Average:46.119; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg1103603106	G -> A	LOC_Os11g07200.2	upstream_gene_variant ; 3913.0bp to feature; MODIFIER	silent_mutation	Average:46.119; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg1103603106	G -> A	LOC_Os11g07190-LOC_Os11g07200	intergenic_region ; MODIFIER	silent_mutation	Average:46.119; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg1103603106	G -> DEL	N	N	silent_mutation	Average:46.119; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1103603106	NA	3.91E-07	mr1471	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
vg1103603106	NA	6.35E-06	mr1642	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
vg1103603106	1.47E-06	1.47E-06	mr1945	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
vg1103603106	NA	3.20E-06	mr1027_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
vg1103603106	NA	5.11E-07	mr1217_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
vg1103603106	NA	2.45E-06	mr1218_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
vg1103603106	NA	2.56E-07	mr1653_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
vg1103603106	NA	4.54E-06	mr1850_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
vg1103603106	1.90E-06	1.90E-06	mr1960_2	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