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Detailed information for vg1114939039:

Variant ID: vg1114939039 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 14939039
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

AACATGCCGAGAGAATGACTGTTCAAAAACCAATCATCTCAACAAAACCCAAACAGCCTTCGCAGCCTAAAAAGGCTTACAAAAGTAGTATAACACCTTT[T/C]
TGTCGGGTACCTTTTTATTTGCATCGTAGTAATTCCAAGGAATTATCTAACTGCGTCAAAAAGGATTTTAACAGCATTGGGCCGTACTGTTGTGAGCAAA

Reverse complement sequence

TTTGCTCACAACAGTACGGCCCAATGCTGTTAAAATCCTTTTTGACGCAGTTAGATAATTCCTTGGAATTACTACGATGCAAATAAAAAGGTACCCGACA[A/G]
AAAGGTGTTATACTACTTTTGTAAGCCTTTTTAGGCTGCGAAGGCTGTTTGGGTTTTGTTGAGATGATTGGTTTTTGAACAGTCATTCTCTCGGCATGTT

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	39.00%	27.60%	2.12%	31.32%	NA
All Indica	2759	50.90%	2.30%	1.88%	44.94%	NA
All Japonica	1512	24.30%	74.30%	0.00%	1.46%	NA
Aus	269	16.00%	0.70%	16.36%	66.91%	NA
Indica I	595	66.40%	4.00%	1.18%	28.40%	NA
Indica II	465	42.60%	1.70%	1.08%	54.62%	NA
Indica III	913	44.00%	0.90%	2.52%	52.57%	NA
Indica Intermediate	786	52.00%	2.90%	2.16%	42.88%	NA
Temperate Japonica	767	38.60%	60.20%	0.00%	1.17%	NA
Tropical Japonica	504	2.80%	95.40%	0.00%	1.79%	NA
Japonica Intermediate	241	23.70%	74.70%	0.00%	1.66%	NA
VI/Aromatic	96	8.30%	84.40%	1.04%	6.25%	NA
Intermediate	90	23.30%	37.80%	3.33%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1114939039	T -> DEL	N	N	silent_mutation	Average:21.126; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N
vg1114939039	T -> C	LOC_Os11g26110.1	upstream_gene_variant ; 442.0bp to feature; MODIFIER	silent_mutation	Average:21.126; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N
vg1114939039	T -> C	LOC_Os11g26120.1	downstream_gene_variant ; 4062.0bp to feature; MODIFIER	silent_mutation	Average:21.126; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N
vg1114939039	T -> C	LOC_Os11g26100-LOC_Os11g26110	intergenic_region ; MODIFIER	silent_mutation	Average:21.126; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1114939039	NA	8.13E-06	mr1382	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
vg1114939039	4.54E-06	NA	mr1728	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