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Detailed information for vg0408293903:

Variant ID: vg0408293903 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 8293903
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGAGAAAACCCTTCGCGGAGGAACTCGAGGTGCAGCTGCGGACGATGATCTCGTATGCAAGCCAACACATGCCCCCCGGCATATCGGCTTGACCGACGA[C/T]
ACTCCTGCTTCAAGGCTTCGTCGATACGTTGACCGATGCCTTCGAGCTGGGTGCAGGCGCCATTCAGCCACGAGATATATCCGGCCGCCGATTCCTCAGG

Reverse complement sequence

CCTGAGGAATCGGCGGCCGGATATATCTCGTGGCTGAATGGCGCCTGCACCCAGCTCGAAGGCATCGGTCAACGTATCGACGAAGCCTTGAAGCAGGAGT[G/A]
TCGTCGGTCAAGCCGATATGCCGGGGGGCATGTGTTGGCTTGCATACGAGATCATCGTCCGCAGCTGCACCTCGAGTTCCTCCGCGAAGGGTTTTCTCGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 38.40% 2.30% 5.71% 53.60% NA
All Indica  2759 13.20% 0.10% 7.00% 79.70% NA
All Japonica  1512 80.00% 6.60% 3.31% 10.12% NA
Aus  269 45.00% 0.00% 4.09% 50.93% NA
Indica I  595 4.00% 0.00% 5.55% 90.42% NA
Indica II  465 36.60% 0.20% 8.17% 55.05% NA
Indica III  913 8.90% 0.10% 8.21% 82.80% NA
Indica Intermediate  786 11.30% 0.10% 5.98% 82.57% NA
Temperate Japonica  767 97.30% 0.00% 0.26% 2.48% NA
Tropical Japonica  504 53.40% 19.80% 7.94% 18.85% NA
Japonica Intermediate  241 80.50% 0.00% 3.32% 16.18% NA
VI/Aromatic  96 74.00% 0.00% 9.38% 16.67% NA
Intermediate  90 53.30% 7.80% 7.78% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0408293903 C -> DEL LOC_Os04g14780.1 N frameshift_variant Average:22.946; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg0408293903 C -> T LOC_Os04g14780.1 missense_variant ; p.Cys497Tyr; MODERATE nonsynonymous_codon ; C497Y Average:22.946; most accessible tissue: Minghui63 panicle, score: 42.799 probably damaging 2.244 DELETERIOUS 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0408293903 1.10E-06 NA mr1016 Jap_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
vg0408293903 8.94E-07 NA mr1017 Jap_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
vg0408293903 7.24E-06 NA mr1019 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
vg0408293903 1.73E-07 NA mr1055 Jap_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
vg0408293903 NA 8.22E-07 mr1136 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
vg0408293903 7.55E-06 NA mr1390 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
vg0408293903 NA 1.34E-06 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
vg0408293903 NA 1.11E-07 mr1583 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
vg0408293903 1.69E-06 NA mr1019_2 Jap_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
vg0408293903 1.24E-07 NA mr1023_2 Jap_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
vg0408293903 5.89E-09 NA mr1055_2 Jap_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
vg0408293903 6.54E-07 NA mr1079_2 Jap_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
vg0408293903 1.87E-09 NA mr1132_2 Jap_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
vg0408293903 1.25E-08 NA mr1390_2 Jap_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
vg0408293903 1.54E-06 NA mr1489_2 Jap_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
vg0408293903 6.50E-09 NA mr1490_2 Jap_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