Search for Variation information by Variation ID:

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

Detailed information for vg0408057094:

Variant ID: vg0408057094 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8057094
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

CATGCTTTGTTCGTTCGTCCGTGTGGAGTCGTTCTTTAGTTTAGAGCCGTTCAGAGCCGCCGGTTCCGTTCGCCGGTTTCAGTTGATCATTTAGGTGATC[T/C]
CGTGTCACGTAGAATTGACTTGTTGAGTCGGTATCTCGTGAGGCTCGCTTGCCAGATCAATCCAAGCCATCCGATCTTGGTCAACTCTCGGTCAAGATTA

Reverse complement sequence

TAATCTTGACCGAGAGTTGACCAAGATCGGATGGCTTGGATTGATCTGGCAAGCGAGCCTCACGAGATACCGACTCAACAAGTCAATTCTACGTGACACG[A/G]
GATCACCTAAATGATCAACTGAAACCGGCGAACGGAACCGGCGGCTCTGAACGGCTCTAAACTAAAGAACGACTCCACACGGACGAACGAACAAAGCATG

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	24.30%	24.20%	4.30%	47.21%	NA
All Indica	2759	7.20%	30.20%	5.98%	56.61%	NA
All Japonica	1512	61.00%	0.70%	1.19%	37.17%	NA
Aus	269	0.40%	97.80%	0.00%	1.86%	NA
Indica I	595	1.80%	10.60%	2.52%	85.04%	NA
Indica II	465	20.20%	15.70%	5.81%	58.28%	NA
Indica III	913	5.70%	52.10%	8.00%	34.17%	NA
Indica Intermediate	786	5.20%	28.20%	6.36%	60.18%	NA
Temperate Japonica	767	94.10%	0.50%	0.65%	4.69%	NA
Tropical Japonica	504	6.90%	1.00%	1.39%	90.67%	NA
Japonica Intermediate	241	68.50%	0.40%	2.49%	28.63%	NA
VI/Aromatic	96	2.10%	24.00%	13.54%	60.42%	NA
Intermediate	90	27.80%	15.60%	7.78%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0408057094	T -> C	LOC_Os04g14390.1	upstream_gene_variant ; 2552.0bp to feature; MODIFIER	silent_mutation	Average:13.335; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0408057094	T -> C	LOC_Os04g14390-LOC_Os04g14400	intergenic_region ; MODIFIER	silent_mutation	Average:13.335; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0408057094	T -> DEL	N	N	silent_mutation	Average:13.335; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408057094	4.88E-06	3.31E-11	mr1722	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