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Detailed information for vg1109870708:

Variant ID: vg1109870708 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9870708
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.58, A: 0.42, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:

CCACGGACGCTCTTCGCACACCACGGAGCAATGCCGAAACATTAGGCAACGTGGCAACGCGCAAGATCCAAGGCCGCAGCAGGGAGCAACTGTCGAAGCA[A/C]
GTCGTGAAGTAGTTCAAGAACAAGCACCCCTAGCCGAACAGCGCCAAGATGCGTAGCGAAGAGTAATCCAAGTGATTACAAGGGCCGACCCGCCAAGCCA

Reverse complement sequence

TGGCTTGGCGGGTCGGCCCTTGTAATCACTTGGATTACTCTTCGCTACGCATCTTGGCGCTGTTCGGCTAGGGGTGCTTGTTCTTGAACTACTTCACGAC[T/G]
TGCTTCGACAGTTGCTCCCTGCTGCGGCCTTGGATCTTGCGCGTTGCCACGTTGCCTAATGTTTCGGCATTGCTCCGTGGTGTGCGAAGAGCGTCCGTGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.20%	6.10%	3.30%	49.49%	NA
All Indica	2759	13.80%	9.60%	4.93%	71.66%	NA
All Japonica	1512	95.90%	0.80%	0.00%	3.31%	NA
Aus	269	19.00%	1.50%	5.95%	73.61%	NA
Indica I	595	24.40%	7.20%	5.88%	62.52%	NA
Indica II	465	8.20%	8.60%	5.81%	77.42%	NA
Indica III	913	3.80%	13.50%	3.40%	79.30%	NA
Indica Intermediate	786	20.60%	7.60%	5.47%	66.28%	NA
Temperate Japonica	767	97.00%	0.00%	0.00%	3.00%	NA
Tropical Japonica	504	94.40%	2.40%	0.00%	3.17%	NA
Japonica Intermediate	241	95.40%	0.00%	0.00%	4.56%	NA
VI/Aromatic	96	22.90%	0.00%	1.04%	76.04%	NA
Intermediate	90	46.70%	4.40%	3.33%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109870708	A -> DEL	N	N	silent_mutation	Average:8.16; most accessible tissue: Callus, score: 29.712	N	N	N	N
vg1109870708	A -> C	LOC_Os11g17690.1	intron_variant ; MODIFIER	silent_mutation	Average:8.16; most accessible tissue: Callus, score: 29.712	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109870708	NA	2.30E-06	mr1928_2	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