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Detailed information for vg1002594715:

Variant ID: vg1002594715 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2594715
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAATGTAGTCAGGCTAATTGGCTACTGCATCGAGAAAAATGCTCCAATGATGGTCATGGAGTATGTGCCTAATAGGGACCTTGATTACCATCTTCATGA[C/G]
AAGAATAGCCTTGATTCATTGGACATAAGATTGGATATTGCTATAGAGTGTGCAGATGCTCTAGGGTATTTACATTCTATGTGCAGCCCTGTTCTACATG

Reverse complement sequence

CATGTAGAACAGGGCTGCACATAGAATGTAAATACCCTAGAGCATCTGCACACTCTATAGCAATATCCAATCTTATGTCCAATGAATCAAGGCTATTCTT[G/C]
TCATGAAGATGGTAATCAAGGTCCCTATTAGGCACATACTCCATGACCATCATTGGAGCATTTTTCTCGATGCAGTAGCCAATTAGCCTGACTACATTTT

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 95.30% 4.50% 0.11% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 86.20% 13.60% 0.20% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 79.50% 20.10% 0.39% 0.00% NA
Tropical Japonica  504 95.80% 4.20% 0.00% 0.00% NA
Japonica Intermediate  241 87.60% 12.40% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 2.22% 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
vg1002594715 C -> G LOC_Os10g05250.1 missense_variant ; p.Asp123Glu; MODERATE nonsynonymous_codon ; D123V Average:51.722; most accessible tissue: Callus, score: 88.03 benign 0.136 TOLERATED 0.40
vg1002594715 C -> G LOC_Os10g05250.1 missense_variant ; p.Asp123Glu; MODERATE nonsynonymous_codon ; D123E Average:51.722; most accessible tissue: Callus, score: 88.03 benign 1.097 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002594715 1.55E-07 NA mr1062 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
vg1002594715 9.84E-06 2.15E-09 mr1062 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
vg1002594715 5.36E-06 5.36E-06 mr1166 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
vg1002594715 NA 2.68E-08 mr1210 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
vg1002594715 NA 1.44E-08 mr1305 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
vg1002594715 1.23E-06 1.23E-06 mr1409 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
vg1002594715 NA 1.23E-06 mr1515 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
vg1002594715 1.22E-06 2.11E-10 mr1585 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
vg1002594715 NA 1.33E-10 mr1585 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
vg1002594715 NA 1.17E-07 mr1586 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
vg1002594715 NA 3.56E-08 mr1765 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
vg1002594715 NA 1.98E-07 mr1305_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
vg1002594715 8.56E-06 1.05E-11 mr1585_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
vg1002594715 NA 1.22E-09 mr1585_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