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Detailed information for vg1125224256:

Variant ID: vg1125224256 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25224256
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTGCTTCCTGCTCCCACCTCATCGCCTCAGGATGCAGCTAGTTTAGGCTGTGCTTAGTTCCTCGGTCAAAAATTTTTTAAGTACACAAACACACATTT[G/A]
AAATATTAAACGTAGACTAATAACAAAACAAATTATAGATTCCGTATGTAAACTGCGAGATGAATTTATTAAGTCTAATTAATTTATCATTAGCGAATGT

Reverse complement sequence

ACATTCGCTAATGATAAATTAATTAGACTTAATAAATTCATCTCGCAGTTTACATACGGAATCTATAATTTGTTTTGTTATTAGTCTACGTTTAATATTT[C/T]
AAATGTGTGTTTGTGTACTTAAAAAATTTTTGACCGAGGAACTAAGCACAGCCTAAACTAGCTGCATCCTGAGGCGATGAGGTGGGAGCAGGAAGCACAT

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	68.00%	31.70%	0.25%	0.00%	NA
All Indica	2759	54.90%	44.80%	0.33%	0.00%	NA
All Japonica	1512	87.40%	12.50%	0.13%	0.00%	NA
Aus	269	79.90%	19.70%	0.37%	0.00%	NA
Indica I	595	40.30%	58.80%	0.84%	0.00%	NA
Indica II	465	93.80%	6.00%	0.22%	0.00%	NA
Indica III	913	44.50%	55.40%	0.11%	0.00%	NA
Indica Intermediate	786	55.00%	44.80%	0.25%	0.00%	NA
Temperate Japonica	767	97.70%	2.20%	0.13%	0.00%	NA
Tropical Japonica	504	71.80%	28.20%	0.00%	0.00%	NA
Japonica Intermediate	241	87.10%	12.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	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
vg1125224256	G -> A	LOC_Os11g41940.1	upstream_gene_variant ; 1412.0bp to feature; MODIFIER	silent_mutation	Average:45.416; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1125224256	G -> A	LOC_Os11g41920.1	downstream_gene_variant ; 1899.0bp to feature; MODIFIER	silent_mutation	Average:45.416; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1125224256	G -> A	LOC_Os11g41920-LOC_Os11g41940	intergenic_region ; MODIFIER	silent_mutation	Average:45.416; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125224256	NA	3.14E-06	mr1159	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
vg1125224256	1.09E-09	NA	mr1191	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
vg1125224256	1.18E-08	1.26E-07	mr1191	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
vg1125224256	NA	1.65E-06	mr1441	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
vg1125224256	NA	3.02E-07	mr1583	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
vg1125224256	9.97E-11	NA	mr1644	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
vg1125224256	7.43E-10	4.65E-08	mr1644	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
vg1125224256	4.40E-06	NA	mr1662	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
vg1125224256	1.15E-07	3.28E-08	mr1794	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
vg1125224256	NA	8.74E-06	mr1150_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
vg1125224256	NA	3.01E-06	mr1159_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
vg1125224256	2.55E-10	NA	mr1191_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
vg1125224256	7.89E-09	2.05E-08	mr1191_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
vg1125224256	NA	5.41E-07	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
vg1125224256	NA	2.61E-08	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
vg1125224256	NA	6.92E-06	mr1895_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
vg1125224256	NA	6.48E-08	mr1933_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