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Detailed information for vg1114010891:

Variant ID: vg1114010891 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 14010891
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

TGGTGAAACCTACTTTGGTCAGCTACCGCTCCCATCAGTTGGCTTCCACTCACCACTGTTATCTCTTCCCAGAAAAAATTATGGGCAGTTTGGTTTGAGG[C/T]
CTAAATTAGGCTTGCCAATTTTTTGGCAACCTCAACAATAATTGTGTATGTTTGGATTGAAACCAAATTTTAGCATACCTATATAACATAGGCCATTTCA

Reverse complement sequence

TGAAATGGCCTATGTTATATAGGTATGCTAAAATTTGGTTTCAATCCAAACATACACAATTATTGTTGAGGTTGCCAAAAAATTGGCAAGCCTAATTTAG[G/A]
CCTCAAACCAAACTGCCCATAATTTTTTCTGGGAAGAGATAACAGTGGTGAGTGGAAGCCAACTGATGGGAGCGGTAGCTGACCAAAGTAGGTTTCACCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.00%	6.60%	0.36%	0.00%	NA
All Indica	2759	99.80%	0.10%	0.04%	0.00%	NA
All Japonica	1512	78.80%	20.20%	1.06%	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%	0.30%	0.13%	0.00%	NA
Temperate Japonica	767	97.80%	1.30%	0.91%	0.00%	NA
Tropical Japonica	504	43.10%	55.40%	1.59%	0.00%	NA
Japonica Intermediate	241	92.90%	6.60%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg1114010891	C -> T	LOC_Os11g24560.1	upstream_gene_variant ; 3889.0bp to feature; MODIFIER	silent_mutation	Average:49.578; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg1114010891	C -> T	LOC_Os11g24540.1	downstream_gene_variant ; 3474.0bp to feature; MODIFIER	silent_mutation	Average:49.578; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg1114010891	C -> T	LOC_Os11g24550.1	downstream_gene_variant ; 516.0bp to feature; MODIFIER	silent_mutation	Average:49.578; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg1114010891	C -> T	LOC_Os11g24540.2	downstream_gene_variant ; 3500.0bp to feature; MODIFIER	silent_mutation	Average:49.578; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg1114010891	C -> T	LOC_Os11g24550-LOC_Os11g24560	intergenic_region ; MODIFIER	silent_mutation	Average:49.578; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1114010891	NA	4.12E-07	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
vg1114010891	2.02E-06	NA	mr1188	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
vg1114010891	NA	1.13E-06	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
vg1114010891	NA	1.45E-07	mr1125_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
vg1114010891	NA	4.56E-07	mr1449_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
vg1114010891	NA	4.73E-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
vg1114010891	NA	9.71E-06	mr1781_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