Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0113762419:

Variant ID: vg0113762419 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 13762419
Reference Allele: TAlternative Allele: TTA,A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCCACAGAGGGAGAAGGATGTGCTAAGACAGGCGCTGGGGAATCGGGAGCATGGAGGCCGGGTTCGAGGCGTATCCTCTAAGCTGAGTTGGAAAGAAGG[T/TTA,A]
TTCAAACAGGACGCCTCCTCATACAAGAAATGTGACGCCTATAAGGACAAGTTGAGGGACGAAGGGGGTAAGCAGTTTGAAAAAGAATTGATTGATTTCT

Reverse complement sequence

AGAAATCAATCAATTCTTTTTCAAACTGCTTACCCCCTTCGTCCCTCAACTTGTCCTTATAGGCGTCACATTTCTTGTATGAGGAGGCGTCCTGTTTGAA[A/TAA,T]
CCTTCTTTCCAACTCAGCTTAGAGGATACGCCTCGAACCCGGCCTCCATGCTCCCGATTCCCCAGCGCCTGTCTTAGCACATCCTTCTCCCTCTGTGGAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.80% 12.30% 2.69% 34.85% TTA: 2.39%
All Indica  2759 26.70% 11.90% 4.24% 54.15% TTA: 3.04%
All Japonica  1512 95.10% 0.30% 0.33% 2.38% TTA: 1.92%
Aus  269 2.20% 88.10% 0.00% 9.67% NA
Indica I  595 31.30% 6.70% 5.04% 46.05% TTA: 10.92%
Indica II  465 19.80% 12.30% 3.23% 63.87% TTA: 0.86%
Indica III  913 26.40% 13.30% 1.86% 58.49% NA
Indica Intermediate  786 27.60% 14.00% 7.00% 49.49% TTA: 1.91%
Temperate Japonica  767 98.60% 0.00% 0.39% 0.26% TTA: 0.78%
Tropical Japonica  504 88.90% 0.80% 0.40% 5.95% TTA: 3.97%
Japonica Intermediate  241 97.10% 0.00% 0.00% 1.66% TTA: 1.24%
VI/Aromatic  96 29.20% 3.10% 3.12% 64.58% NA
Intermediate  90 55.60% 10.00% 2.22% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0113762419 T -> A LOC_Os01g24410.1 synonymous_variant ; p.Gly177Gly; LOW synonymous_codon Average:22.446; most accessible tissue: Zhenshan97 flag leaf, score: 52.255 N N N N
vg0113762419 T -> TTA LOC_Os01g24410.1 frameshift_variant ; p.Phe178fs; HIGH frameshift_variant Average:22.446; most accessible tissue: Zhenshan97 flag leaf, score: 52.255 N N N N
vg0113762419 T -> DEL LOC_Os01g24410.1 N frameshift_variant Average:22.446; most accessible tissue: Zhenshan97 flag leaf, score: 52.255 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113762419 NA 2.68E-07 mr1028 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
vg0113762419 NA 2.26E-06 mr1126 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
vg0113762419 NA 2.01E-07 mr1369 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
vg0113762419 NA 1.26E-08 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
vg0113762419 NA 4.19E-07 mr1453 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
vg0113762419 NA 5.58E-07 mr1574 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
vg0113762419 3.35E-06 3.36E-06 mr1674 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
vg0113762419 NA 1.00E-05 mr1952 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