Search for Variation information by Variation ID:

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

Detailed information for vg0720195420:

Variant ID: vg0720195420 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 20195420
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, C: 0.05, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

CTTGACCACAAAACCCGGGTATGACCCGTCCCCCAACTTACGAAAACCGGGTAAACGTGGTCCCTCGGCGGTTTTGAAGGTGGTTTTGGCTGACGTGGCG[T/C]
CTACGTGGCTTGTTTGACTTGGTTTTCGTCCCACGTGCCATTGACGTGGCGCTTACGTGGCAATTATATCTCGGAAAAATAATAAAAAGCGTGGCCCCAC

Reverse complement sequence

GTGGGGCCACGCTTTTTATTATTTTTCCGAGATATAATTGCCACGTAAGCGCCACGTCAATGGCACGTGGGACGAAAACCAAGTCAAACAAGCCACGTAG[A/G]
CGCCACGTCAGCCAAAACCACCTTCAAAACCGCCGAGGGACCACGTTTACCCGGTTTTCGTAAGTTGGGGGACGGGTCATACCCGGGTTTTGTGGTCAAG

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	40.60%	11.00%	0.57%	47.82%	NA
All Indica	2759	15.20%	17.40%	0.80%	66.65%	NA
All Japonica	1512	72.60%	2.60%	0.26%	24.47%	NA
Aus	269	97.40%	0.00%	0.00%	2.60%	NA
Indica I	595	12.30%	19.00%	1.51%	67.23%	NA
Indica II	465	16.80%	4.90%	0.43%	77.85%	NA
Indica III	913	11.30%	26.30%	0.66%	61.77%	NA
Indica Intermediate	786	21.00%	13.10%	0.64%	65.27%	NA
Temperate Japonica	767	96.60%	0.00%	0.13%	3.26%	NA
Tropical Japonica	504	33.50%	7.50%	0.60%	58.33%	NA
Japonica Intermediate	241	78.00%	0.80%	0.00%	21.16%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	47.80%	3.30%	1.11%	47.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0720195420	T -> DEL	N	N	silent_mutation	Average:84.431; most accessible tissue: Minghui63 young leaf, score: 94.991	N	N	N	N
vg0720195420	T -> C	LOC_Os07g33770.1	upstream_gene_variant ; 442.0bp to feature; MODIFIER	silent_mutation	Average:84.431; most accessible tissue: Minghui63 young leaf, score: 94.991	N	N	N	N
vg0720195420	T -> C	LOC_Os07g33770-LOC_Os07g33780	intergenic_region ; MODIFIER	silent_mutation	Average:84.431; most accessible tissue: Minghui63 young leaf, score: 94.991	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0720195420	NA	1.06E-06	mr1243	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
vg0720195420	NA	2.17E-08	mr1364	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
vg0720195420	NA	1.32E-06	mr1364	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
vg0720195420	NA	4.26E-23	mr1422	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
vg0720195420	NA	1.53E-07	mr1422	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
vg0720195420	NA	5.97E-09	mr1443	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
vg0720195420	NA	7.28E-08	mr1443	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
vg0720195420	NA	4.68E-10	mr1539	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
vg0720195420	NA	3.27E-14	mr1540	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
vg0720195420	NA	5.18E-18	mr1583	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
vg0720195420	NA	2.34E-14	mr1732	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
vg0720195420	NA	1.21E-10	mr1228_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
vg0720195420	NA	8.07E-27	mr1422_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
vg0720195420	NA	2.20E-17	mr1540_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
vg0720195420	NA	3.24E-16	mr1583_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
vg0720195420	NA	3.60E-07	mr1696_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
vg0720195420	NA	5.54E-18	mr1732_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
vg0720195420	NA	5.86E-08	mr1879_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