Search for Variation information by Variation ID:

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

Detailed information for vg1209004488:

Variant ID: vg1209004488 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9004488
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.65, C: 0.35, others allele: 0.00, population size: 54. )

Flanking Sequence (100 bp) in Reference Genome:

ACCGGTCGGCAGTGATGACGGCGGCCAGCGATGAAGGTGTAGATGCCCAACAACGGTGGTGTGACCAACCAACCGTGTAGGCGAGGACACTAGTTGACAG[T/C]
GGACGAGGCGGCCGGTCAGTGAAGACGATGATGTCCATCAGCAGCGGCGCAATATGCCAGCCGTGAAGGCGAAGAGGCTTGTCGACGGAAGATGAGGCAG

Reverse complement sequence

CTGCCTCATCTTCCGTCGACAAGCCTCTTCGCCTTCACGGCTGGCATATTGCGCCGCTGCTGATGGACATCATCGTCTTCACTGACCGGCCGCCTCGTCC[A/G]
CTGTCAACTAGTGTCCTCGCCTACACGGTTGGTTGGTCACACCACCGTTGTTGGGCATCTACACCTTCATCGCTGGCCGCCGTCATCACTGCCGACCGGT

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	39.70%	37.90%	0.47%	21.94%	NA
All Indica	2759	54.00%	10.00%	0.80%	35.19%	NA
All Japonica	1512	4.40%	94.60%	0.00%	1.06%	NA
Aus	269	80.70%	5.60%	0.00%	13.75%	NA
Indica I	595	36.30%	20.50%	1.01%	42.18%	NA
Indica II	465	51.80%	11.80%	0.65%	35.70%	NA
Indica III	913	65.20%	2.40%	0.44%	31.98%	NA
Indica Intermediate	786	55.70%	9.80%	1.15%	33.33%	NA
Temperate Japonica	767	6.00%	93.00%	0.00%	1.04%	NA
Tropical Japonica	504	3.40%	95.80%	0.00%	0.79%	NA
Japonica Intermediate	241	1.20%	97.10%	0.00%	1.66%	NA
VI/Aromatic	96	72.90%	22.90%	0.00%	4.17%	NA
Intermediate	90	36.70%	53.30%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209004488	T -> C	LOC_Os12g15770.1	synonymous_variant ; p.Pro50Pro; LOW	synonymous_codon	Average:44.166; most accessible tissue: Callus, score: 82.589	N	N	N	N
vg1209004488	T -> DEL	LOC_Os12g15770.1	N	frameshift_variant	Average:44.166; most accessible tissue: Callus, score: 82.589	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209004488	NA	1.53E-08	mr1425	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
vg1209004488	NA	1.01E-07	mr1659	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