Search for Variation information by Variation ID:

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

Detailed information for vg0401900537:

Variant ID: vg0401900537 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1900537
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, A: 0.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCTCCTCCTCAGGAGAGAGAGGCGGTTCACTTCGTTTGCCCCGTGAAACATAGAAGCATTGCATCGCTGTCAACCACAGTAGTGCACGTGCTTTCCAT[A/C]
TCTTATAATTAGAACTATCAAAAGCATGTGGTTTCAGTGTTGCAGCAAAGCCAACTACCGAAAATGACCTATCAGGTTTTTGGATTGTTGGAAATTTGGT

Reverse complement sequence

ACCAAATTTCCAACAATCCAAAAACCTGATAGGTCATTTTCGGTAGTTGGCTTTGCTGCAACACTGAAACCACATGCTTTTGATAGTTCTAATTATAAGA[T/G]
ATGGAAAGCACGTGCACTACTGTGGTTGACAGCGATGCAATGCTTCTATGTTTCACGGGGCAAACGAAGTGAACCGCCTCTCTCTCCTGAGGAGGAGGCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.70%	9.30%	14.58%	7.41%	NA
All Indica	2759	80.80%	0.60%	16.67%	1.88%	NA
All Japonica	1512	45.60%	27.30%	9.39%	17.72%	NA
Aus	269	64.30%	0.70%	25.65%	9.29%	NA
Indica I	595	95.80%	0.30%	2.69%	1.18%	NA
Indica II	465	69.50%	1.10%	25.38%	4.09%	NA
Indica III	913	74.00%	0.10%	25.30%	0.55%	NA
Indica Intermediate	786	84.10%	1.10%	12.09%	2.67%	NA
Temperate Japonica	767	17.20%	44.60%	6.78%	31.42%	NA
Tropical Japonica	504	79.00%	3.60%	15.08%	2.38%	NA
Japonica Intermediate	241	66.00%	22.00%	5.81%	6.22%	NA
VI/Aromatic	96	89.60%	0.00%	8.33%	2.08%	NA
Intermediate	90	75.60%	10.00%	11.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401900537	A -> C	LOC_Os04g04120.1	missense_variant ; p.Ile186Arg; MODERATE	nonsynonymous_codon ; I186R	Average:26.518; most accessible tissue: Zhenshan97 root, score: 54.262	probably damaging	-2.13	TOLERATED	1.00
vg0401900537	A -> DEL	LOC_Os04g04120.1	N	frameshift_variant	Average:26.518; most accessible tissue: Zhenshan97 root, score: 54.262	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401900537	NA	9.38E-08	mr1002	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
vg0401900537	NA	3.09E-06	mr1002	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
vg0401900537	1.36E-08	6.80E-17	mr1182	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
vg0401900537	NA	4.37E-09	mr1182	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
vg0401900537	9.44E-08	8.32E-15	mr1282	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
vg0401900537	NA	1.61E-08	mr1282	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
vg0401900537	3.14E-08	4.46E-16	mr1650	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
vg0401900537	NA	6.11E-08	mr1650	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
vg0401900537	1.45E-06	1.07E-12	mr1658	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
vg0401900537	NA	2.11E-07	mr1658	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
vg0401900537	NA	4.39E-07	mr1805	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
vg0401900537	NA	6.28E-07	mr1880	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
vg0401900537	NA	5.80E-11	mr1282_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
vg0401900537	NA	7.23E-07	mr1880_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