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Detailed information for vg1117980116:

Variant ID: vg1117980116 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17980116
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

CAAAATTACATTAAAATTTCAGTACATACACTTCACACATATCCCATTGTTATCACCAAAATTTGATAGGGTTCTTTACTAGATTCGGTTAGGAAAGAAA[C/T]
CGATTGGTAAATGAAAGTTTATTTTGATAAGGCCGAGTTCAAGAGGAATTGTGAAGACCCTGGCAAAGCAATTTCATATTTTCTTAGTATATCTCTTAAG

Reverse complement sequence

CTTAAGAGATATACTAAGAAAATATGAAATTGCTTTGCCAGGGTCTTCACAATTCCTCTTGAACTCGGCCTTATCAAAATAAACTTTCATTTACCAATCG[G/A]
TTTCTTTCCTAACCGAATCTAGTAAAGAACCCTATCAAATTTTGGTGATAACAATGGGATATGTGTGAAGTGTATGTACTGAAATTTTAATGTAATTTTG

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	61.70%	31.60%	0.23%	6.50%	NA
All Indica	2759	40.20%	52.50%	0.14%	7.18%	NA
All Japonica	1512	95.80%	0.90%	0.07%	3.24%	NA
Aus	269	88.80%	0.00%	0.74%	10.41%	NA
Indica I	595	27.70%	64.20%	0.00%	8.07%	NA
Indica II	465	40.40%	58.50%	0.00%	1.08%	NA
Indica III	913	45.20%	44.60%	0.11%	10.08%	NA
Indica Intermediate	786	43.50%	49.40%	0.38%	6.74%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	91.30%	0.40%	0.20%	8.13%	NA
Japonica Intermediate	241	94.60%	2.10%	0.00%	3.32%	NA
VI/Aromatic	96	69.80%	1.00%	3.12%	26.04%	NA
Intermediate	90	57.80%	33.30%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117980116	C -> T	LOC_Os11g30910.1	upstream_gene_variant ; 4848.0bp to feature; MODIFIER	silent_mutation	Average:38.66; most accessible tissue: Zhenshan97 young leaf, score: 59.612	N	N	N	N
vg1117980116	C -> T	LOC_Os11g30880-LOC_Os11g30910	intergenic_region ; MODIFIER	silent_mutation	Average:38.66; most accessible tissue: Zhenshan97 young leaf, score: 59.612	N	N	N	N
vg1117980116	C -> DEL	N	N	silent_mutation	Average:38.66; most accessible tissue: Zhenshan97 young leaf, score: 59.612	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117980116	5.03E-08	3.88E-06	mr1800	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
vg1117980116	2.70E-07	1.23E-07	mr1800	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