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Detailed information for vg1127978095:

Variant ID: vg1127978095 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27978095
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.05, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTTAAGCGTGACACAAATAATCAAGCGGATAAACTTTTCGGAAGAGTGACAAGTATAATATGTTTAAGATAAATTAAATGCAGTCATTAGTTTCGAA[T/C]
GGGTCTTATTAAGTTTGGGAGTAGGTGAATTTTGGAGCGTGGCACTATAAATGAAACGAAAAGGTACACCCTATCCAACATAAAGTACAATTTAATTTCT

Reverse complement sequence

AGAAATTAAATTGTACTTTATGTTGGATAGGGTGTACCTTTTCGTTTCATTTATAGTGCCACGCTCCAAAATTCACCTACTCCCAAACTTAATAAGACCC[A/G]
TTCGAAACTAATGACTGCATTTAATTTATCTTAAACATATTATACTTGTCACTCTTCCGAAAAGTTTATCCGCTTGATTATTTGTGTCACGCTTAAAAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	26.10%	25.80%	0.89%	47.27%	NA
All Indica	2759	17.50%	33.00%	0.76%	48.75%	NA
All Japonica	1512	38.00%	13.80%	1.06%	47.22%	NA
Aus	269	47.20%	23.00%	1.12%	28.62%	NA
Indica I	595	15.10%	43.00%	0.84%	41.01%	NA
Indica II	465	12.90%	3.40%	0.43%	83.23%	NA
Indica III	913	17.90%	48.70%	0.66%	32.75%	NA
Indica Intermediate	786	21.60%	24.60%	1.02%	52.80%	NA
Temperate Japonica	767	27.20%	19.70%	0.78%	52.28%	NA
Tropical Japonica	504	53.00%	6.00%	1.39%	39.68%	NA
Japonica Intermediate	241	40.70%	11.20%	1.24%	46.89%	NA
VI/Aromatic	96	8.30%	26.00%	0.00%	65.62%	NA
Intermediate	90	45.60%	13.30%	2.22%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127978095	T -> DEL	N	N	silent_mutation	Average:22.67; most accessible tissue: Callus, score: 65.82	N	N	N	N
vg1127978095	T -> C	LOC_Os11g46190.1	upstream_gene_variant ; 3260.0bp to feature; MODIFIER	silent_mutation	Average:22.67; most accessible tissue: Callus, score: 65.82	N	N	N	N
vg1127978095	T -> C	LOC_Os11g46200.1	downstream_gene_variant ; 273.0bp to feature; MODIFIER	silent_mutation	Average:22.67; most accessible tissue: Callus, score: 65.82	N	N	N	N
vg1127978095	T -> C	LOC_Os11g46190-LOC_Os11g46200	intergenic_region ; MODIFIER	silent_mutation	Average:22.67; most accessible tissue: Callus, score: 65.82	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127978095	NA	3.00E-07	mr1083	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
vg1127978095	NA	7.97E-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
vg1127978095	1.91E-06	NA	mr1174	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
vg1127978095	NA	6.56E-09	mr1345	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
vg1127978095	NA	2.46E-06	mr1345	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
vg1127978095	NA	1.49E-06	mr1427	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
vg1127978095	NA	5.09E-06	mr1560	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
vg1127978095	NA	3.11E-06	mr1634	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