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Detailed information for vg0711021713:

Variant ID: vg0711021713 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 11021713
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGTTTACTTGAGAAGAAGGAGGATGAAGCACCTGGGATGACTAAAGATAGTTTGCAAGGTAAATTAAATGGTGTTGAGATAAATAAAGGTGAGTATACT[C/T]
AAGGTGAGCTACACATGTCCACTTTTCATGGTATAGTAGAGCAACCATTAGTGGAACCAACTGCTGAGATTCCTTTGTCACAAGTGGATTTATTTGCTGT

Reverse complement sequence

ACAGCAAATAAATCCACTTGTGACAAAGGAATCTCAGCAGTTGGTTCCACTAATGGTTGCTCTACTATACCATGAAAAGTGGACATGTGTAGCTCACCTT[G/A]
AGTATACTCACCTTTATTTATCTCAACACCATTTAATTTACCTTGCAAACTATCTTTAGTCATCCCAGGTGCTTCATCCTCCTTCTTCTCAAGTAAACTA

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 63.70% 27.00% 0.42% 8.91% NA
All Indica  2759 96.80% 0.90% 0.18% 2.07% NA
All Japonica  1512 1.90% 79.00% 0.60% 18.52% NA
Aus  269 90.70% 4.50% 0.00% 4.83% NA
Indica I  595 99.50% 0.20% 0.17% 0.17% NA
Indica II  465 96.80% 3.00% 0.00% 0.22% NA
Indica III  913 99.80% 0.10% 0.00% 0.11% NA
Indica Intermediate  786 91.30% 1.30% 0.51% 6.87% NA
Temperate Japonica  767 2.00% 65.80% 1.04% 31.16% NA
Tropical Japonica  504 0.80% 98.60% 0.00% 0.60% NA
Japonica Intermediate  241 4.10% 79.70% 0.41% 15.77% NA
VI/Aromatic  96 19.80% 7.30% 4.17% 68.75% NA
Intermediate  90 52.20% 40.00% 2.22% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0711021713 C -> DEL LOC_Os07g18640.1 N frameshift_variant Average:27.515; most accessible tissue: Callus, score: 45.572 N N N N
vg0711021713 C -> T LOC_Os07g18640.1 stop_gained ; p.Gln135*; HIGH stop_gained Average:27.515; most accessible tissue: Callus, score: 45.572 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0711021713 2.03E-06 2.22E-11 mr1578 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
vg0711021713 NA 6.51E-14 mr1592 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
vg0711021713 NA 2.23E-36 mr1828 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
vg0711021713 NA 1.82E-10 mr1905 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
vg0711021713 NA 9.89E-15 mr1579_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
vg0711021713 NA 9.85E-11 mr1986_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