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Detailed information for vg1122336770:

Variant ID: vg1122336770 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22336770
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.54, C: 0.46, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

TGAGACGCACTTGGCCTTATTTTTTTAGACCGGCGATCGAATAAAGTCGATTGCATTGCACAGGCGAATAAAATTTATCACCTCTAGTGCCGCACTACCG[A/C]
TAGTACAGACGCTTTTGACTCCAACACGAAAAAAATTCATCTTTCTCGTCATATCAACTCGCACCATCCTGAGTGACTCATCCATGTTCCTGATGCCTTC

Reverse complement sequence

GAAGGCATCAGGAACATGGATGAGTCACTCAGGATGGTGCGAGTTGATATGACGAGAAAGATGAATTTTTTTCGTGTTGGAGTCAAAAGCGTCTGTACTA[T/G]
CGGTAGTGCGGCACTAGAGGTGATAAATTTTATTCGCCTGTGCAATGCAATCGACTTTATTCGATCGCCGGTCTAAAAAAATAAGGCCAAGTGCGTCTCA

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	20.30%	15.30%	0.38%	63.94%	NA
All Indica	2759	4.30%	10.30%	0.58%	84.81%	NA
All Japonica	1512	52.60%	20.10%	0.00%	27.31%	NA
Aus	269	3.70%	21.20%	0.00%	75.09%	NA
Indica I	595	6.60%	10.80%	0.50%	82.18%	NA
Indica II	465	5.80%	2.40%	1.08%	90.75%	NA
Indica III	913	0.90%	16.40%	0.44%	82.26%	NA
Indica Intermediate	786	5.60%	7.60%	0.51%	86.26%	NA
Temperate Japonica	767	79.40%	7.30%	0.00%	13.30%	NA
Tropical Japonica	504	17.30%	44.60%	0.00%	38.10%	NA
Japonica Intermediate	241	41.10%	9.50%	0.00%	49.38%	NA
VI/Aromatic	96	17.70%	62.50%	1.04%	18.75%	NA
Intermediate	90	23.30%	21.10%	1.11%	54.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122336770	A -> DEL	N	N	silent_mutation	Average:14.063; most accessible tissue: Callus, score: 92.071	N	N	N	N
vg1122336770	A -> C	LOC_Os11g37759.1	downstream_gene_variant ; 2692.0bp to feature; MODIFIER	silent_mutation	Average:14.063; most accessible tissue: Callus, score: 92.071	N	N	N	N
vg1122336770	A -> C	LOC_Os11g37770.1	downstream_gene_variant ; 3141.0bp to feature; MODIFIER	silent_mutation	Average:14.063; most accessible tissue: Callus, score: 92.071	N	N	N	N
vg1122336770	A -> C	LOC_Os11g37759.3	downstream_gene_variant ; 2706.0bp to feature; MODIFIER	silent_mutation	Average:14.063; most accessible tissue: Callus, score: 92.071	N	N	N	N
vg1122336770	A -> C	LOC_Os11g37759.2	downstream_gene_variant ; 2689.0bp to feature; MODIFIER	silent_mutation	Average:14.063; most accessible tissue: Callus, score: 92.071	N	N	N	N
vg1122336770	A -> C	LOC_Os11g37759-LOC_Os11g37770	intergenic_region ; MODIFIER	silent_mutation	Average:14.063; most accessible tissue: Callus, score: 92.071	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122336770	3.60E-06	3.48E-07	mr1824	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