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Detailed information for vg1113972556:

Variant ID: vg1113972556 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 13972556
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

TACCTTTACCGTAGCGAAGGTCAAGTCATTTGCATATGTGATTGTGAATCTGCAAATCAATAATACTTTAAAATGAAAGTGTAATTGTGGAAAAAAGTTT[G/T]
CATACTCAGATAATTATTTCCTATGCCTTTTGTTACAGTAACAAACTATATATCTGCAAGTTATAAATTCTCACCCTGCAGACTGCCCATCGATATGCCA

Reverse complement sequence

TGGCATATCGATGGGCAGTCTGCAGGGTGAGAATTTATAACTTGCAGATATATAGTTTGTTACTGTAACAAAAGGCATAGGAAATAATTATCTGAGTATG[C/A]
AAACTTTTTTCCACAATTACACTTTCATTTTAAAGTATTATTGATTTGCAGATTCACAATCACATATGCAAATGACTTGACCTTCGCTACGGTAAAGGTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.90%	4.80%	0.30%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	84.90%	14.20%	0.93%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	99.50%	0.40%	0.13%	0.00%	NA
Tropical Japonica	504	56.70%	41.30%	1.98%	0.00%	NA
Japonica Intermediate	241	97.10%	1.70%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg1113972556	G -> T	LOC_Os11g24500.1	upstream_gene_variant ; 1472.0bp to feature; MODIFIER	silent_mutation	Average:59.026; most accessible tissue: Callus, score: 75.996	N	N	N	N
vg1113972556	G -> T	LOC_Os11g24510.1	intron_variant ; MODIFIER	silent_mutation	Average:59.026; most accessible tissue: Callus, score: 75.996	N	N	N	N
vg1113972556	G -> T	LOC_Os11g24510.2	intron_variant ; MODIFIER	silent_mutation	Average:59.026; most accessible tissue: Callus, score: 75.996	N	N	N	N
vg1113972556	G -> T	LOC_Os11g24510.3	intron_variant ; MODIFIER	silent_mutation	Average:59.026; most accessible tissue: Callus, score: 75.996	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1113972556	NA	1.66E-06	mr1125	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
vg1113972556	NA	3.86E-12	mr1248	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
vg1113972556	NA	5.04E-07	mr1578	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
vg1113972556	NA	7.49E-07	mr1676	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
vg1113972556	NA	9.55E-06	mr1379_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
vg1113972556	NA	3.28E-07	mr1632_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
vg1113972556	NA	2.51E-07	mr1696_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
vg1113972556	NA	2.04E-06	mr1905_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