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Detailed information for vg1117693473:

Variant ID: vg1117693473 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17693473
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

AACCGGGACTAAAAATGATCTTTATTCCCGGTTGGTGTTACCAACCGGGACTAAAGATCAAAATTTTTTTAACCGGAACTAAAAATGATCTTTAGTCCCG[G/A]
TTTTATTGCAACCGAGACTATTGTGAAATTTAGTCGACCGACCAAATATGATTTCTCCACCAGTGGTAGCAAGTATACACCGTATACTCCGTGGACATGG

Reverse complement sequence

CCATGTCCACGGAGTATACGGTGTATACTTGCTACCACTGGTGGAGAAATCATATTTGGTCGGTCGACTAAATTTCACAATAGTCTCGGTTGCAATAAAA[C/T]
CGGGACTAAAGATCATTTTTAGTTCCGGTTAAAAAAATTTTGATCTTTAGTCCCGGTTGGTAACACCAACCGGGAATAAAGATCATTTTTAGTCCCGGTT

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	76.70%	23.20%	0.04%	0.00%	NA
All Indica	2759	74.80%	25.20%	0.04%	0.00%	NA
All Japonica	1512	77.20%	22.80%	0.00%	0.00%	NA
Aus	269	87.00%	12.60%	0.37%	0.00%	NA
Indica I	595	96.60%	3.40%	0.00%	0.00%	NA
Indica II	465	53.50%	46.50%	0.00%	0.00%	NA
Indica III	913	73.40%	26.50%	0.11%	0.00%	NA
Indica Intermediate	786	72.50%	27.50%	0.00%	0.00%	NA
Temperate Japonica	767	98.40%	1.60%	0.00%	0.00%	NA
Tropical Japonica	504	39.90%	60.10%	0.00%	0.00%	NA
Japonica Intermediate	241	87.60%	12.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	73.30%	26.70%	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
vg1117693473	G -> A	LOC_Os11g30430.1	upstream_gene_variant ; 1384.0bp to feature; MODIFIER	silent_mutation	Average:61.628; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N
vg1117693473	G -> A	LOC_Os11g30410-LOC_Os11g30430	intergenic_region ; MODIFIER	silent_mutation	Average:61.628; most accessible tissue: Zhenshan97 panicle, score: 79.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117693473	NA	2.37E-14	Grain_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1117693473	NA	1.91E-09	mr1016	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
vg1117693473	NA	1.47E-09	mr1018	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
vg1117693473	NA	3.84E-09	mr1019	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
vg1117693473	NA	1.56E-06	mr1050	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
vg1117693473	NA	4.45E-11	mr1055	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
vg1117693473	NA	2.65E-06	mr1155	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
vg1117693473	NA	1.20E-07	mr1271	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
vg1117693473	NA	8.88E-06	mr1378	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
vg1117693473	NA	2.46E-06	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
vg1117693473	NA	1.11E-06	mr1543	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
vg1117693473	NA	4.11E-11	mr1668	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
vg1117693473	NA	5.54E-08	mr1668	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
vg1117693473	NA	5.36E-13	mr1769	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
vg1117693473	NA	6.05E-06	mr1887	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
vg1117693473	NA	3.30E-07	mr1951	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
vg1117693473	NA	3.16E-10	mr1019_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
vg1117693473	NA	4.59E-10	mr1347_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
vg1117693473	NA	1.15E-06	mr1629_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