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Detailed information for vg1127387533:

Variant ID: vg1127387533 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27387533
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, C: 0.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

CTACATTTTGTACAAGAATTTATTGCACTCTCCTCAAGGTGATGAAACTGATTAAGAATTTATTGCACTTACAAGACGAATGTTGGTATGAAGAACACTA[G/C]
CTTAATGCTTTCATAATTTGATTGCCCTTCAAATCGGTTTAACTTGCTCTGCTAGAATTCTAGAACTGCCTAAACAGTGGTGCCCATGTTGGACTATGAA

Reverse complement sequence

TTCATAGTCCAACATGGGCACCACTGTTTAGGCAGTTCTAGAATTCTAGCAGAGCAAGTTAAACCGATTTGAAGGGCAATCAAATTATGAAAGCATTAAG[C/G]
TAGTGTTCTTCATACCAACATTCGTCTTGTAAGTGCAATAAATTCTTAATCAGTTTCATCACCTTGAGGAGAGTGCAATAAATTCTTGTACAAAATGTAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.50%	14.30%	0.04%	0.19%	NA
All Indica	2759	86.80%	13.00%	0.00%	0.18%	NA
All Japonica	1512	82.90%	16.80%	0.07%	0.20%	NA
Aus	269	89.60%	10.40%	0.00%	0.00%	NA
Indica I	595	97.60%	2.40%	0.00%	0.00%	NA
Indica II	465	93.50%	6.50%	0.00%	0.00%	NA
Indica III	913	77.90%	22.00%	0.00%	0.11%	NA
Indica Intermediate	786	85.10%	14.40%	0.00%	0.51%	NA
Temperate Japonica	767	93.20%	6.60%	0.13%	0.00%	NA
Tropical Japonica	504	73.00%	26.60%	0.00%	0.40%	NA
Japonica Intermediate	241	71.00%	28.60%	0.00%	0.41%	NA
VI/Aromatic	96	80.20%	18.80%	1.04%	0.00%	NA
Intermediate	90	78.90%	20.00%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127387533	G -> DEL	N	N	silent_mutation	Average:50.086; most accessible tissue: Callus, score: 79.996	N	N	N	N
vg1127387533	G -> C	LOC_Os11g45260.1	upstream_gene_variant ; 2577.0bp to feature; MODIFIER	silent_mutation	Average:50.086; most accessible tissue: Callus, score: 79.996	N	N	N	N
vg1127387533	G -> C	LOC_Os11g45250.1	intron_variant ; MODIFIER	silent_mutation	Average:50.086; most accessible tissue: Callus, score: 79.996	N	N	N	N
vg1127387533	G -> C	LOC_Os11g45250.2	intron_variant ; MODIFIER	silent_mutation	Average:50.086; most accessible tissue: Callus, score: 79.996	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127387533	4.18E-06	NA	mr1133_2	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
vg1127387533	6.45E-06	3.13E-07	mr1133_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