Search for Variation information by Variation ID:

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

Detailed information for vg1110072677:

Variant ID: vg1110072677 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10072677
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCAAACAATTTGGTAGGGCACATTTTGGCTTCAAATCAAAATGGCCCAATATCTTCATATAGTACCCTCAGATTTTGTAGAACCATTTGAGAGTATCCTC[C/T]
ATTGGGGGTAGAGTTTCCTATATGTGGCTTTAGACAGTATGGCCCACATGACGCTACTACTACCCGTGCCTTACATTGTATAATACATGTAACACTTTTA

Reverse complement sequence

TAAAAGTGTTACATGTATTATACAATGTAAGGCACGGGTAGTAGTAGCGTCATGTGGGCCATACTGTCTAAAGCCACATATAGGAAACTCTACCCCCAAT[G/A]
GAGGATACTCTCAAATGGTTCTACAAAATCTGAGGGTACTATATGAAGATATTGGGCCATTTTGATTTGAAGCCAAAATGTGCCCTACCAAATTGTTTGG

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	62.70%	37.00%	0.23%	0.00%	NA
All Indica	2759	91.50%	8.30%	0.18%	0.00%	NA
All Japonica	1512	5.40%	94.20%	0.40%	0.00%	NA
Aus	269	84.80%	15.20%	0.00%	0.00%	NA
Indica I	595	90.40%	9.40%	0.17%	0.00%	NA
Indica II	465	98.70%	1.10%	0.22%	0.00%	NA
Indica III	913	97.20%	2.70%	0.11%	0.00%	NA
Indica Intermediate	786	81.60%	18.20%	0.25%	0.00%	NA
Temperate Japonica	767	3.00%	96.90%	0.13%	0.00%	NA
Tropical Japonica	504	8.90%	90.70%	0.40%	0.00%	NA
Japonica Intermediate	241	5.40%	93.40%	1.24%	0.00%	NA
VI/Aromatic	96	80.20%	19.80%	0.00%	0.00%	NA
Intermediate	90	60.00%	40.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110072677	C -> T	LOC_Os11g17940.1	upstream_gene_variant ; 3179.0bp to feature; MODIFIER	silent_mutation	Average:65.922; most accessible tissue: Zhenshan97 root, score: 75.661	N	N	N	N
vg1110072677	C -> T	LOC_Os11g17930.1	downstream_gene_variant ; 2933.0bp to feature; MODIFIER	silent_mutation	Average:65.922; most accessible tissue: Zhenshan97 root, score: 75.661	N	N	N	N
vg1110072677	C -> T	LOC_Os11g17930-LOC_Os11g17940	intergenic_region ; MODIFIER	silent_mutation	Average:65.922; most accessible tissue: Zhenshan97 root, score: 75.661	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110072677	NA	1.36E-10	mr1595	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
vg1110072677	1.72E-06	NA	mr1973	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
vg1110072677	NA	1.83E-06	mr1517_2	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