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Detailed information for vg1120296077:

Variant ID: vg1120296077 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20296077
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.02, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

TTGCTAGCAACATATTTAATTTCTCTCTACATGTATATAAACATGGACGAAGCTGAAACGAATATTAACATACTCCCTCCGTCCCAAAAAAAGACAAACC[C/A]
TGGTTTCCGTGTCCAATGTTTGACCGTCCTTCTTATTTGAAAAAAATATGAAAAAAATAAAAAGATAAGTCACGCATAAAGTATTAATCATGTTTTATCA

Reverse complement sequence

TGATAAAACATGATTAATACTTTATGCGTGACTTATCTTTTTATTTTTTTCATATTTTTTTCAAATAAGAAGGACGGTCAAACATTGGACACGGAAACCA[G/T]
GGTTTGTCTTTTTTTGGGACGGAGGGAGTATGTTAATATTCGTTTCAGCTTCGTCCATGTTTATATACATGTAGAGAGAAATTAAATATGTTGCTAGCAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.30%	12.00%	0.59%	43.14%	NA
All Indica	2759	26.90%	17.30%	0.69%	55.13%	NA
All Japonica	1512	63.20%	4.70%	0.13%	32.01%	NA
Aus	269	96.70%	0.00%	1.86%	1.49%	NA
Indica I	595	30.40%	0.80%	0.50%	68.24%	NA
Indica II	465	24.70%	33.10%	0.86%	41.29%	NA
Indica III	913	26.20%	19.70%	0.44%	53.67%	NA
Indica Intermediate	786	26.20%	17.70%	1.02%	55.09%	NA
Temperate Japonica	767	82.50%	2.30%	0.00%	15.12%	NA
Tropical Japonica	504	47.40%	9.50%	0.20%	42.86%	NA
Japonica Intermediate	241	34.40%	2.10%	0.41%	63.07%	NA
VI/Aromatic	96	94.80%	0.00%	2.08%	3.12%	NA
Intermediate	90	50.00%	20.00%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120296077	C -> A	LOC_Os11g34660.1	intron_variant ; MODIFIER	silent_mutation	Average:15.195; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1120296077	C -> DEL	N	N	silent_mutation	Average:15.195; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120296077	4.24E-07	NA	mr1770	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
vg1120296077	NA	2.34E-07	mr1795_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