Search for Variation information by Variation ID:

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

Detailed information for vg0906306952:

Variant ID: vg0906306952 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6306952
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACATCACCGTGAATTCATACAGCCCATATCGCGTGGTGAATGCGGTCTTCGGGATATCTTCTTCACGAATACACAATTGGTGATATCTGGAACGAAGATC[G/A]
ATTTTAGAAAACACAGTGGCACCTTTAAGCTGATCGAACAGATCATCGATCTGGGGAAGAGGGTACTTGTTTTTGATAGTAACTTCATTAAGAGCTCTGT

Reverse complement sequence

ACAGAGCTCTTAATGAAGTTACTATCAAAAACAAGTACCCTCTTCCCCAGATCGATGATCTGTTCGATCAGCTTAAAGGTGCCACTGTGTTTTCTAAAAT[C/T]
GATCTTCGTTCCAGATATCACCAATTGTGTATTCGTGAAGAAGATATCCCGAAGACCGCATTCACCACGCGATATGGGCTGTATGAATTCACGGTGATGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.80%	4.60%	2.84%	21.75%	NA
All Indica	2759	64.30%	0.40%	1.70%	33.56%	NA
All Japonica	1512	84.30%	12.00%	1.59%	2.12%	NA
Aus	269	69.50%	0.40%	16.73%	13.38%	NA
Indica I	595	51.10%	0.20%	2.18%	46.55%	NA
Indica II	465	66.50%	0.00%	1.72%	31.83%	NA
Indica III	913	72.40%	0.50%	1.64%	25.41%	NA
Indica Intermediate	786	63.70%	0.60%	1.40%	34.22%	NA
Temperate Japonica	767	95.40%	2.50%	1.17%	0.91%	NA
Tropical Japonica	504	68.30%	28.40%	2.18%	1.19%	NA
Japonica Intermediate	241	82.20%	8.30%	1.66%	7.88%	NA
VI/Aromatic	96	52.10%	12.50%	16.67%	18.75%	NA
Intermediate	90	67.80%	12.20%	2.22%	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
vg0906306952	G -> DEL	LOC_Os09g11360.1	N	frameshift_variant	Average:30.334; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N
vg0906306952	G -> A	LOC_Os09g11360.1	synonymous_variant ; p.Ile798Ile; LOW	synonymous_codon	Average:30.334; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906306952	NA	5.39E-06	mr1179	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
vg0906306952	NA	1.69E-06	mr1248	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
vg0906306952	NA	1.19E-14	mr1410	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
vg0906306952	NA	9.08E-06	mr1543	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
vg0906306952	NA	7.52E-07	mr1642	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
vg0906306952	NA	5.35E-06	mr1039_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
vg0906306952	NA	1.38E-19	mr1301_2	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
vg0906306952	NA	5.29E-16	mr1410_2	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
vg0906306952	NA	1.53E-06	mr1422_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
vg0906306952	NA	2.65E-07	mr1554_2	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
vg0906306952	8.01E-07	9.21E-08	mr1849_2	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
vg0906306952	NA	2.31E-06	mr1849_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
vg0906306952	5.82E-06	NA	mr1850_2	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
vg0906306952	NA	2.38E-06	mr1873_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
vg0906306952	NA	2.56E-09	mr1916_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