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Detailed information for vg0722959446:

Variant ID: vg0722959446 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22959446
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, G: 0.05, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


ATATTTTGATTTCTGATCAACAATAAGTATTGTCTACACAATACTTACTCCCTTCAGTAAAGAAAAAGGTAAATTGTGATTCTCGGAGTCAAGACAATGC[C/G]
CACTTTGACCACTAGATTATAACATCATATGCCCTGAGAAAAGTACATTGACCACTGATATCATGCAAGTACTTTTCATACAAATTGACCAATCAAGGCA

Reverse complement sequence

TGCCTTGATTGGTCAATTTGTATGAAAAGTACTTGCATGATATCAGTGGTCAATGTACTTTTCTCAGGGCATATGATGTTATAATCTAGTGGTCAAAGTG[G/C]
GCATTGTCTTGACTCCGAGAATCACAATTTACCTTTTTCTTTACTGAAGGGAGTAAGTATTGTGTAGACAATACTTATTGTTGATCAGAAATCAAAATAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.30% 46.20% 0.23% 0.25% NA
All Indica  2759 30.60% 68.60% 0.36% 0.43% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 1.50% 98.50% 0.00% 0.00% NA
Indica I  595 4.50% 95.00% 0.34% 0.17% NA
Indica II  465 47.70% 50.30% 1.29% 0.65% NA
Indica III  913 39.10% 60.40% 0.11% 0.44% NA
Indica Intermediate  786 30.20% 69.20% 0.13% 0.51% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 77.80% 21.10% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0722959446 C -> DEL N N silent_mutation Average:56.649; most accessible tissue: Callus, score: 71.597 N N N N
vg0722959446 C -> G LOC_Os07g38260.1 upstream_gene_variant ; 4627.0bp to feature; MODIFIER silent_mutation Average:56.649; most accessible tissue: Callus, score: 71.597 N N N N
vg0722959446 C -> G LOC_Os07g38270.1 intron_variant ; MODIFIER silent_mutation Average:56.649; most accessible tissue: Callus, score: 71.597 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0722959446 NA 1.29E-17 mr1133 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
vg0722959446 NA 8.55E-16 mr1146 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
vg0722959446 NA 1.35E-06 mr1209 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
vg0722959446 NA 9.43E-13 mr1222 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
vg0722959446 NA 6.48E-09 mr1275 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
vg0722959446 NA 1.35E-06 mr1420 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
vg0722959446 NA 3.08E-09 mr1439 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
vg0722959446 NA 8.32E-13 mr1441 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
vg0722959446 NA 1.82E-09 mr1442 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
vg0722959446 NA 1.82E-12 mr1667 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
vg0722959446 NA 3.57E-07 mr1764 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
vg0722959446 NA 3.12E-09 mr1986 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
vg0722959446 NA 1.67E-19 mr1146_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
vg0722959446 NA 1.09E-33 mr1150_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
vg0722959446 NA 5.10E-10 mr1222_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
vg0722959446 NA 2.87E-18 mr1239_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
vg0722959446 NA 7.85E-08 mr1607_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
vg0722959446 NA 1.19E-06 mr1863_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