Search for Variation information by Variation ID:

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

Detailed information for vg1213796013:

Variant ID: vg1213796013 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13796013
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTGGCCAACGGCGACATCGACCTCGCCAGATGGTATATCTCTGCCGGAGTCCTCCGAGAACGAGCAAAACCCTCACGGAGAAATTCGAGGTCCAGGCG[C/T]
GGGCGATGATCTCGTAGGCAAGCCAACACATGCCCTCCGGCGTATCGGCTCGATTGACGACACTCCTGCTTCAAGGCCTCGTCGATACGCTTGCCGATGC

Reverse complement sequence

GCATCGGCAAGCGTATCGACGAGGCCTTGAAGCAGGAGTGTCGTCAATCGAGCCGATACGCCGGAGGGCATGTGTTGGCTTGCCTACGAGATCATCGCCC[G/A]
CGCCTGGACCTCGAATTTCTCCGTGAGGGTTTTGCTCGTTCTCGGAGGACTCCGGCAGAGATATACCATCTGGCGAGGTCGATGTCGCCGTTGGCCAAGA

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	81.80%	4.50%	3.87%	9.88%	NA
All Indica	2759	96.80%	1.30%	0.54%	1.34%	NA
All Japonica	1512	53.00%	10.90%	9.72%	26.39%	NA
Aus	269	93.30%	0.00%	0.74%	5.95%	NA
Indica I	595	97.00%	1.00%	0.00%	2.02%	NA
Indica II	465	94.20%	1.30%	1.51%	3.01%	NA
Indica III	913	99.00%	0.90%	0.11%	0.00%	NA
Indica Intermediate	786	95.80%	1.90%	0.89%	1.40%	NA
Temperate Japonica	767	81.20%	1.40%	1.43%	15.91%	NA
Tropical Japonica	504	18.80%	24.40%	19.84%	36.90%	NA
Japonica Intermediate	241	34.40%	12.90%	14.94%	37.76%	NA
VI/Aromatic	96	68.80%	5.20%	17.71%	8.33%	NA
Intermediate	90	83.30%	6.70%	2.22%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213796013	C -> DEL	N	N	silent_mutation	Average:19.223; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1213796013	C -> T	LOC_Os12g24200.1	downstream_gene_variant ; 1510.0bp to feature; MODIFIER	silent_mutation	Average:19.223; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N
vg1213796013	C -> T	LOC_Os12g24210.1	intron_variant ; MODIFIER	silent_mutation	Average:19.223; most accessible tissue: Zhenshan97 panicle, score: 32.308	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213796013	6.00E-07	6.00E-07	mr1276	Ind_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