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Detailed information for vg1120378562:

Variant ID: vg1120378562 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20378562
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.60, C: 0.40, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

AGCACCGGCATCCCTATGCCCATGCAAGAGCAGAGAGCGAGAGGAAGGAAGGAAGGAGAGAAACAGAGAAAGAGAAGAGGGGAAAGAGAGTAGGTGGTGA[C/T]
GTGGACATAATGATGGGTCCAAGTGGGTCTCACGCAGACTCAGCCACTATGTTGGATAAAACCAGAGTCAAAACCTCTGAAGGGCCTAAAGTGAACGGTT

Reverse complement sequence

AACCGTTCACTTTAGGCCCTTCAGAGGTTTTGACTCTGGTTTTATCCAACATAGTGGCTGAGTCTGCGTGAGACCCACTTGGACCCATCATTATGTCCAC[G/A]
TCACCACCTACTCTCTTTCCCCTCTTCTCTTTCTCTGTTTCTCTCCTTCCTTCCTTCCTCTCGCTCTCTGCTCTTGCATGGGCATAGGGATGCCGGTGCT

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	22.50%	13.00%	0.53%	63.99%	NA
All Indica	2759	2.20%	13.30%	0.76%	83.76%	NA
All Japonica	1512	59.50%	6.40%	0.07%	33.99%	NA
Aus	269	0.70%	49.80%	0.37%	49.07%	NA
Indica I	595	2.50%	1.20%	0.34%	95.97%	NA
Indica II	465	2.80%	5.40%	0.43%	91.40%	NA
Indica III	913	0.90%	27.30%	1.64%	70.21%	NA
Indica Intermediate	786	3.20%	10.80%	0.25%	85.75%	NA
Temperate Japonica	767	78.10%	4.70%	0.00%	17.21%	NA
Tropical Japonica	504	45.40%	9.10%	0.20%	45.24%	NA
Japonica Intermediate	241	29.90%	6.20%	0.00%	63.90%	NA
VI/Aromatic	96	71.90%	10.40%	0.00%	17.71%	NA
Intermediate	90	34.40%	7.80%	2.22%	55.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120378562	C -> T	LOC_Os11g34770.1	upstream_gene_variant ; 2430.0bp to feature; MODIFIER	silent_mutation	Average:17.294; most accessible tissue: Callus, score: 82.34	N	N	N	N
vg1120378562	C -> T	LOC_Os11g34790.1	upstream_gene_variant ; 3273.0bp to feature; MODIFIER	silent_mutation	Average:17.294; most accessible tissue: Callus, score: 82.34	N	N	N	N
vg1120378562	C -> T	LOC_Os11g34780.1	downstream_gene_variant ; 353.0bp to feature; MODIFIER	silent_mutation	Average:17.294; most accessible tissue: Callus, score: 82.34	N	N	N	N
vg1120378562	C -> T	LOC_Os11g34780-LOC_Os11g34790	intergenic_region ; MODIFIER	silent_mutation	Average:17.294; most accessible tissue: Callus, score: 82.34	N	N	N	N
vg1120378562	C -> DEL	N	N	silent_mutation	Average:17.294; most accessible tissue: Callus, score: 82.34	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120378562	1.44E-06	NA	mr1503	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
vg1120378562	NA	2.93E-06	mr1807	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