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Detailed information for vg0501807498:

Variant ID: vg0501807498 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1807498
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGACATATAAAAATTATTAATAAAACACCAAATATAATCCTAATGATGATTAAAAGGAGGGACGACAAGCAGGCCGTGAAGTAAACGAGCAAGGCGGTTA[C/T]
CGGGACTTTTAGAAAGTAAAAAAAAATAAACCTCATTGATAATCATATTCGATTTTTAAAATCTCAATGACAATAAAAAGGAGAAGCAGCGGGCGGGGTG

Reverse complement sequence

CACCCCGCCCGCTGCTTCTCCTTTTTATTGTCATTGAGATTTTAAAAATCGAATATGATTATCAATGAGGTTTATTTTTTTTTACTTTCTAAAAGTCCCG[G/A]
TAACCGCCTTGCTCGTTTACTTCACGGCCTGCTTGTCGTCCCTCCTTTTAATCATCATTAGGATTATATTTGGTGTTTTATTAATAATTTTTATATGTCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.60% 24.80% 2.84% 34.72% NA
All Indica  2759 61.80% 11.50% 2.90% 23.89% NA
All Japonica  1512 1.70% 48.50% 2.25% 47.55% NA
Aus  269 8.20% 4.10% 4.46% 83.27% NA
Indica I  595 97.80% 2.20% 0.00% 0.00% NA
Indica II  465 66.00% 12.50% 1.08% 20.43% NA
Indica III  913 32.50% 17.50% 7.34% 42.61% NA
Indica Intermediate  786 65.90% 10.80% 1.02% 22.26% NA
Temperate Japonica  767 1.00% 73.00% 0.78% 25.16% NA
Tropical Japonica  504 1.60% 22.60% 1.98% 73.81% NA
Japonica Intermediate  241 3.70% 24.90% 7.47% 63.90% NA
VI/Aromatic  96 3.10% 87.50% 2.08% 7.29% NA
Intermediate  90 25.60% 32.20% 6.67% 35.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0501807498 C -> T LOC_Os05g04020.1 intron_variant ; MODIFIER silent_mutation Average:17.11; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg0501807498 C -> DEL N N silent_mutation Average:17.11; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501807498 NA 2.82E-13 mr1531 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
vg0501807498 NA 3.77E-16 mr1807 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
vg0501807498 7.53E-07 2.25E-07 mr1030_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
vg0501807498 2.35E-06 3.26E-06 mr1030_2 Ind_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
vg0501807498 NA 8.12E-07 mr1358_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
vg0501807498 NA 1.31E-07 mr1446_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
vg0501807498 NA 6.25E-06 mr1524_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
vg0501807498 NA 2.83E-07 mr1527_2 Ind_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
vg0501807498 8.53E-06 1.90E-16 mr1578_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
vg0501807498 8.44E-06 1.59E-09 mr1754_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
vg0501807498 NA 3.02E-06 mr1754_2 Ind_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
vg0501807498 NA 1.27E-07 mr1819_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
vg0501807498 NA 1.16E-06 mr1910_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
vg0501807498 NA 2.23E-10 mr1946_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
vg0501807498 NA 2.23E-10 mr1948_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
vg0501807498 5.19E-06 NA mr1952_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
vg0501807498 2.36E-06 2.53E-08 mr1952_2 Ind_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
vg0501807498 NA 9.78E-06 mr1957_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
vg0501807498 2.09E-06 NA mr1965_2 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
vg0501807498 5.73E-06 5.73E-06 mr1965_2 Ind_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