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Detailed information for vg0819075122:

Variant ID: vg0819075122 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19075122
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTATCACTTTTTCTATTGTAAATTTGGTACCTAGGTACTATGAGGTATCATGAGGTAACAAAAAAAATAATGTAAAATTTGGTACCTCATTGTACCTCCT[T/C]
AAGGACCGTAAAATTGCTCTAAAGTTTATGGTTTGAAACTAAAATAGTCAAAATAATTATGAAATAGGGAAGCTGGATTATCAAAATTCCTTTCTACCGT

Reverse complement sequence

ACGGTAGAAAGGAATTTTGATAATCCAGCTTCCCTATTTCATAATTATTTTGACTATTTTAGTTTCAAACCATAAACTTTAGAGCAATTTTACGGTCCTT[A/G]
AGGAGGTACAATGAGGTACCAAATTTTACATTATTTTTTTTGTTACCTCATGATACCTCATAGTACCTAGGTACCAAATTTACAATAGAAAAAGTGATAC

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 85.10% 13.20% 1.42% 0.28% NA
All Indica  2759 98.30% 1.10% 0.14% 0.47% NA
All Japonica  1512 61.40% 34.50% 4.10% 0.00% NA
Aus  269 94.10% 5.90% 0.00% 0.00% NA
Indica I  595 96.80% 2.70% 0.50% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 97.90% 0.70% 0.00% 1.42% NA
Indica Intermediate  786 99.00% 0.90% 0.13% 0.00% NA
Temperate Japonica  767 36.20% 58.80% 4.95% 0.00% NA
Tropical Japonica  504 94.80% 3.60% 1.59% 0.00% NA
Japonica Intermediate  241 71.40% 22.00% 6.64% 0.00% NA
VI/Aromatic  96 63.50% 35.40% 1.04% 0.00% NA
Intermediate  90 76.70% 23.30% 0.00% 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
vg0819075122 T -> C LOC_Os08g30900.1 intron_variant ; MODIFIER silent_mutation Average:43.482; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0819075122 T -> C LOC_Os08g30900.2 intron_variant ; MODIFIER silent_mutation Average:43.482; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0819075122 T -> DEL N N silent_mutation Average:43.482; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819075122 7.90E-06 NA mr1057_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
vg0819075122 NA 1.20E-08 mr1182_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
vg0819075122 3.00E-07 NA mr1261_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
vg0819075122 NA 5.08E-10 mr1282_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
vg0819075122 NA 4.06E-07 mr1282_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
vg0819075122 NA 1.65E-06 mr1330_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
vg0819075122 NA 5.91E-10 mr1530_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
vg0819075122 8.72E-07 4.76E-18 mr1980_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
vg0819075122 NA 8.38E-08 mr1980_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