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Detailed information for vg1122345222:

Variant ID: vg1122345222 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22345222
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.04, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

CTGAACAGAACTAGCCCGTGACGCTTCAAATTAACCTGTTAATCGATACCAGTCCCAGGAAACAGTGCTGGTATCACAGGAAGACAGAATATCACAGCAA[T/C]
AGAGGTCTTTTTATTACAGAGTAGGAGTACAGTTATGTTGGGCTGCGGACAGATTCCGAGCTCACAACTGCATTACAAAAGGAAAAGCGGAAGCCAAGAC

Reverse complement sequence

GTCTTGGCTTCCGCTTTTCCTTTTGTAATGCAGTTGTGAGCTCGGAATCTGTCCGCAGCCCAACATAACTGTACTCCTACTCTGTAATAAAAAGACCTCT[A/G]
TTGCTGTGATATTCTGTCTTCCTGTGATACCAGCACTGTTTCCTGGGACTGGTATCGATTAACAGGTTAATTTGAAGCGTCACGGGCTAGTTCTGTTCAG

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	25.30%	16.00%	5.01%	53.70%	NA
All Indica	2759	10.40%	10.30%	5.44%	73.87%	NA
All Japonica	1512	49.60%	18.70%	3.90%	27.84%	NA
Aus	269	20.80%	67.30%	5.95%	5.95%	NA
Indica I	595	7.40%	3.50%	5.04%	84.03%	NA
Indica II	465	3.00%	13.30%	5.16%	78.49%	NA
Indica III	913	16.60%	13.10%	6.02%	64.18%	NA
Indica Intermediate	786	9.70%	10.40%	5.22%	74.68%	NA
Temperate Japonica	767	45.90%	33.50%	6.13%	14.47%	NA
Tropical Japonica	504	59.90%	0.60%	1.79%	37.70%	NA
Japonica Intermediate	241	39.80%	9.10%	1.24%	49.79%	NA
VI/Aromatic	96	76.00%	2.10%	5.21%	16.67%	NA
Intermediate	90	35.60%	4.40%	7.78%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122345222	T -> DEL	N	N	silent_mutation	Average:8.827; most accessible tissue: Callus, score: 25.623	N	N	N	N
vg1122345222	T -> C	LOC_Os11g37770.1	upstream_gene_variant ; 4505.0bp to feature; MODIFIER	silent_mutation	Average:8.827; most accessible tissue: Callus, score: 25.623	N	N	N	N
vg1122345222	T -> C	LOC_Os11g37770-LOC_Os11g37774	intergenic_region ; MODIFIER	silent_mutation	Average:8.827; most accessible tissue: Callus, score: 25.623	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122345222	2.45E-06	2.79E-06	mr1669	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
vg1122345222	NA	4.51E-06	mr1740	Jap_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