Search for Variation information by Variation ID:

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

Detailed information for vg1217862937:

Variant ID: vg1217862937 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17862937
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTTTGGTGTGTTTTGGATTTTTTCGGAGTTTTCTGAAACTCATTTTCGGACTTTCCGAAAACACACAGAACCAGATTTTCGCTTCTGGAAATTTTTGGA[T/C]
ATGTCCGAAAGTGATTTTCGGACTTTCCGAAAAGGACTGCGAAGGCAAAAGTGGTTCTGTATATTTTCGGACTTGTTCGAAACTGATTTTCGGATCTTTC

Reverse complement sequence

GAAAGATCCGAAAATCAGTTTCGAACAAGTCCGAAAATATACAGAACCACTTTTGCCTTCGCAGTCCTTTTCGGAAAGTCCGAAAATCACTTTCGGACAT[A/G]
TCCAAAAATTTCCAGAAGCGAAAATCTGGTTCTGTGTGTTTTCGGAAAGTCCGAAAATGAGTTTCAGAAAACTCCGAAAAAATCCAAAACACACCAAACT

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	72.00%	3.20%	0.99%	23.76%	NA
All Indica	2759	71.60%	3.90%	1.30%	23.20%	NA
All Japonica	1512	75.80%	2.80%	0.60%	20.77%	NA
Aus	269	61.00%	0.00%	0.74%	38.29%	NA
Indica I	595	93.80%	0.30%	0.00%	5.88%	NA
Indica II	465	60.20%	0.90%	1.29%	37.63%	NA
Indica III	913	59.50%	7.60%	2.63%	30.34%	NA
Indica Intermediate	786	75.70%	4.10%	0.76%	19.47%	NA
Temperate Japonica	767	98.00%	0.00%	0.00%	1.96%	NA
Tropical Japonica	504	47.80%	7.90%	1.59%	42.66%	NA
Japonica Intermediate	241	63.50%	1.20%	0.41%	34.85%	NA
VI/Aromatic	96	47.90%	0.00%	0.00%	52.08%	NA
Intermediate	90	81.10%	1.10%	0.00%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217862937	T -> C	LOC_Os12g29874.1	upstream_gene_variant ; 1218.0bp to feature; MODIFIER	silent_mutation	Average:12.916; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg1217862937	T -> C	LOC_Os12g29860.1	downstream_gene_variant ; 734.0bp to feature; MODIFIER	silent_mutation	Average:12.916; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg1217862937	T -> C	LOC_Os12g29860-LOC_Os12g29874	intergenic_region ; MODIFIER	silent_mutation	Average:12.916; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg1217862937	T -> DEL	N	N	silent_mutation	Average:12.916; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217862937	8.97E-06	8.66E-07	mr1039	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
vg1217862937	NA	1.24E-06	mr1114	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
vg1217862937	NA	4.39E-06	mr1116	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
vg1217862937	6.02E-06	6.02E-06	mr1266	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
vg1217862937	8.43E-06	8.43E-06	mr1275	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
vg1217862937	NA	6.01E-06	mr1345	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
vg1217862937	8.04E-07	8.04E-07	mr1365	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
vg1217862937	NA	2.60E-06	mr1695	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
vg1217862937	9.00E-07	9.00E-07	mr1823	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
vg1217862937	2.59E-07	2.59E-07	mr1876	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