Search for Variation information by Variation ID:

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

Detailed information for vg0817806989:

Variant ID: vg0817806989 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17806989
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACAGAACCACCACAGCCTACGAAGTCGGAGCCTACAGGAGCCAAGTTGCTGGGGTGATCTAGTCGAGCCAACTCGACTACGGTCTCGTCAGTATCATCGA[T/G]
TTCTGCTATTCCCTTTGTAATCTGTGGCTTCCATTATATAATCCCATATCAACTGGATTAGGGCTATTACCTATTAAGGGGCCTGAACCAGTATAATCCT

Reverse complement sequence

AGGATTATACTGGTTCAGGCCCCTTAATAGGTAATAGCCCTAATCCAGTTGATATGGGATTATATAATGGAAGCCACAGATTACAAAGGGAATAGCAGAA[A/C]
TCGATGATACTGACGAGACCGTAGTCGAGTTGGCTCGACTAGATCACCCCAGCAACTTGGCTCCTGTAGGCTCCGACTTCGTAGGCTGTGGTGGTTCTGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	26.30%	0.10%	1.12%	72.47%	NA
All Indica	2759	5.50%	0.10%	1.56%	92.79%	NA
All Japonica	1512	54.80%	0.00%	0.46%	44.78%	NA
Aus	269	86.20%	0.00%	0.37%	13.38%	NA
Indica I	595	3.90%	0.00%	2.18%	93.95%	NA
Indica II	465	6.20%	0.40%	0.43%	92.90%	NA
Indica III	913	3.90%	0.00%	0.77%	95.29%	NA
Indica Intermediate	786	8.30%	0.10%	2.67%	88.93%	NA
Temperate Japonica	767	82.80%	0.00%	0.52%	16.69%	NA
Tropical Japonica	504	21.60%	0.00%	0.00%	78.37%	NA
Japonica Intermediate	241	34.90%	0.00%	1.24%	63.90%	NA
VI/Aromatic	96	5.20%	0.00%	0.00%	94.79%	NA
Intermediate	90	30.00%	0.00%	2.22%	67.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817806989	T -> G	LOC_Os08g29080.1	upstream_gene_variant ; 779.0bp to feature; MODIFIER	silent_mutation	Average:16.798; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0817806989	T -> G	LOC_Os08g29080-LOC_Os08g29090	intergenic_region ; MODIFIER	silent_mutation	Average:16.798; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0817806989	T -> DEL	N	N	silent_mutation	Average:16.798; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817806989	3.13E-07	1.40E-06	mr1086	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
vg0817806989	6.21E-06	6.21E-06	mr1076_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