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Detailed information for vg1117078119:

Variant ID: vg1117078119 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17078119
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.22, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TAGCCCACATTGTTGTAATCACCTTTCTCTCAAATCCTCCAAGGACCCTCTACATAATTAAGCAGCAACCTATAGAAAACATGCTGTGTCAACCATGAAA[T/C]
AGCAGCAGTTAATTACTAATTAATGTTTAATTACATATAAGATACGCACATGCATCCTTCAACTAAACAATACAGTGTGTTGATATGAAAATTGGTCATT

Reverse complement sequence

AATGACCAATTTTCATATCAACACACTGTATTGTTTAGTTGAAGGATGCATGTGCGTATCTTATATGTAATTAAACATTAATTAGTAATTAACTGCTGCT[A/G]
TTTCATGGTTGACACAGCATGTTTTCTATAGGTTGCTGCTTAATTATGTAGAGGGTCCTTGGAGGATTTGAGAGAAAGGTGATTACAACAATGTGGGCTA

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	65.80%	34.10%	0.04%	0.00%	NA
All Indica	2759	97.00%	2.90%	0.04%	0.00%	NA
All Japonica	1512	9.50%	90.50%	0.00%	0.00%	NA
Aus	269	85.10%	14.90%	0.00%	0.00%	NA
Indica I	595	91.60%	8.40%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	96.70%	3.20%	0.13%	0.00%	NA
Temperate Japonica	767	3.00%	97.00%	0.00%	0.00%	NA
Tropical Japonica	504	19.60%	80.40%	0.00%	0.00%	NA
Japonica Intermediate	241	9.10%	90.90%	0.00%	0.00%	NA
VI/Aromatic	96	7.30%	92.70%	0.00%	0.00%	NA
Intermediate	90	61.10%	37.80%	1.11%	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
vg1117078119	T -> C	LOC_Os11g29420.1	downstream_gene_variant ; 2104.0bp to feature; MODIFIER	silent_mutation	Average:55.709; most accessible tissue: Zhenshan97 root, score: 80.68	N	N	N	N
vg1117078119	T -> C	LOC_Os11g29410.1	intron_variant ; MODIFIER	silent_mutation	Average:55.709; most accessible tissue: Zhenshan97 root, score: 80.68	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117078119	NA	1.55E-14	mr1376	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
vg1117078119	3.33E-06	NA	mr1390	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
vg1117078119	NA	1.55E-14	mr1431	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
vg1117078119	NA	3.16E-21	mr1839	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