Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1122839038:

Variant ID: vg1122839038 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22839038
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACGGGATGGGGCGAGGCGTGTGTCAGACCGTCTGTCGCCACCTAACCCACGATCTGATCGGTCTGCGACTGGTCACAGACCGGATAAACGAGCGCGCTG[T/C]
ACTGCGTTACATGCGGCGTGACGCGCTCGTCCAAATCGCAATAAATGCGGTTAGGTGAGCCCTGCTGCGCTCACCTAACCCATACACGCGGCGCGAAACC

Reverse complement sequence

GGTTTCGCGCCGCGTGTATGGGTTAGGTGAGCGCAGCAGGGCTCACCTAACCGCATTTATTGCGATTTGGACGAGCGCGTCACGCCGCATGTAACGCAGT[A/G]
CAGCGCGCTCGTTTATCCGGTCTGTGACCAGTCGCAGACCGATCAGATCGTGGGTTAGGTGGCGACAGACGGTCTGACACACGCCTCGCCCCATCCCGTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	17.80%	0.50%	14.09%	67.65%	NA
All Indica	2759	4.10%	0.80%	18.19%	76.91%	NA
All Japonica	1512	45.00%	0.00%	6.08%	48.88%	NA
Aus	269	10.80%	0.00%	4.46%	84.76%	NA
Indica I	595	6.40%	1.70%	5.88%	86.05%	NA
Indica II	465	3.40%	0.90%	5.38%	90.32%	NA
Indica III	913	2.50%	0.30%	39.43%	57.72%	NA
Indica Intermediate	786	4.70%	0.50%	10.43%	84.35%	NA
Temperate Japonica	767	52.30%	0.00%	1.30%	46.41%	NA
Tropical Japonica	504	46.40%	0.00%	9.33%	44.25%	NA
Japonica Intermediate	241	19.10%	0.00%	14.52%	66.39%	NA
VI/Aromatic	96	3.10%	1.00%	53.12%	42.71%	NA
Intermediate	90	15.60%	0.00%	10.00%	74.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122839038	T -> DEL	N	N	silent_mutation	Average:17.44; most accessible tissue: Callus, score: 35.876	N	N	N	N
vg1122839038	T -> C	LOC_Os11g38540.1	upstream_gene_variant ; 820.0bp to feature; MODIFIER	silent_mutation	Average:17.44; most accessible tissue: Callus, score: 35.876	N	N	N	N
vg1122839038	T -> C	LOC_Os11g38550.1	downstream_gene_variant ; 3466.0bp to feature; MODIFIER	silent_mutation	Average:17.44; most accessible tissue: Callus, score: 35.876	N	N	N	N
vg1122839038	T -> C	LOC_Os11g38540-LOC_Os11g38550	intergenic_region ; MODIFIER	silent_mutation	Average:17.44; most accessible tissue: Callus, score: 35.876	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122839038	NA	1.41E-07	mr1517_2	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
vg1122839038	6.24E-06	5.13E-09	mr1538_2	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
vg1122839038	9.89E-07	9.89E-07	mr1541_2	Jap_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