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Detailed information for vg1120307856:

Variant ID: vg1120307856 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 20307856
Reference Allele: C	Alternative Allele: T,CAT
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, T: 0.15, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGATGATATTTTGATCTAGGTGGGTTAATAAATTTTCAATTCCCGTGATTGTCTACACTCCATTAAAACATCCGTTCTTTTCAATACTCTATTTTACA[C/T,CAT]
GAGTATTCCTATCATATTTTTTACCTTTTCTATTTTTTTTTCAATCATGTGTTATGAAGGAACCTTTAACTTTTTTTCACCGAGAGGCAAAGTCATAAAA

Reverse complement sequence

TTTTATGACTTTGCCTCTCGGTGAAAAAAAGTTAAAGGTTCCTTCATAACACATGATTGAAAAAAAAATAGAAAAGGTAAAAAATATGATAGGAATACTC[G/A,ATG]
TGTAAAATAGAGTATTGAAAAGAACGGATGTTTTAATGGAGTGTAGACAATCACGGGAATTGAAAATTTATTAACCCACCTAGATCAAAATATCATCTAT

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	28.50%	24.50%	2.88%	42.47%	CAT: 1.63%
All Indica	2759	35.70%	3.50%	4.75%	53.46%	CAT: 2.61%
All Japonica	1512	5.70%	62.00%	0.13%	32.14%	NA
Aus	269	91.80%	1.50%	0.74%	4.09%	CAT: 1.86%
Indica I	595	25.70%	5.20%	1.34%	67.73%	NA
Indica II	465	52.90%	2.80%	4.73%	39.35%	CAT: 0.22%
Indica III	913	33.30%	1.10%	6.13%	52.68%	CAT: 6.79%
Indica Intermediate	786	35.80%	5.50%	5.73%	51.91%	CAT: 1.15%
Temperate Japonica	767	4.40%	80.40%	0.00%	15.12%	NA
Tropical Japonica	504	9.50%	47.40%	0.40%	42.66%	NA
Japonica Intermediate	241	1.70%	34.00%	0.00%	64.32%	NA
VI/Aromatic	96	1.00%	89.60%	0.00%	9.38%	NA
Intermediate	90	31.10%	38.90%	1.11%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120307856	C -> CAT	LOC_Os11g34660.1	intron_variant ; MODIFIER	silent_mutation	Average:20.331; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg1120307856	C -> T	LOC_Os11g34660.1	intron_variant ; MODIFIER	silent_mutation	Average:20.331; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg1120307856	C -> DEL	N	N	silent_mutation	Average:20.331; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120307856	1.11E-06	1.11E-06	mr1239	Ind_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