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Detailed information for vg0207333714:

Variant ID: vg0207333714 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 7333714
Reference Allele: CAlternative Allele: T,CTAATTTACCG
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTACTCCGCCGCCACCCCCAACCTGTCCGGCCTCGTCGTCGCCGCCGCCGCCCCACCCTGCTCACATCACATCACATCACATCATATATCTGTCTCCTAT[C/T,CTAATTTACCG]
TAATTTACCGTAATCTCATGTATACCCTGGTATCAATTGCTGACAACCTTTTATTTTATAAGGCGTAGAATTAAACATGATCGCAACACCCAAATTCAAC

Reverse complement sequence

GTTGAATTTGGGTGTTGCGATCATGTTTAATTCTACGCCTTATAAAATAAAAGGTTGTCAGCAATTGATACCAGGGTATACATGAGATTACGGTAAATTA[G/A,CGGTAAATTAG]
ATAGGAGACAGATATATGATGTGATGTGATGTGATGTGAGCAGGGTGGGGCGGCGGCGGCGACGACGAGGCCGGACAGGTTGGGGGTGGCGGCGGAGTAC

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 97.90% 1.80% 0.32% 0.00% CTAATTTACCG: 0.02%
All Indica  2759 100.00% 0.00% 0.00% 0.00% CTAATTTACCG: 0.04%
All Japonica  1512 93.80% 5.20% 0.93% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.00% 0.00% CTAATTTACCG: 0.11%
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 97.90% 0.50% 1.56% 0.00% NA
Tropical Japonica  504 88.30% 11.70% 0.00% 0.00% NA
Japonica Intermediate  241 92.50% 6.60% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 1.11% 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
vg0207333714 C -> CTAATTTACCG LOC_Os02g13670.1 intron_variant ; MODIFIER silent_mutation Average:72.612; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N
vg0207333714 C -> T LOC_Os02g13670.1 intron_variant ; MODIFIER silent_mutation Average:72.612; most accessible tissue: Zhenshan97 panicle, score: 86.432 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0207333714 2.13E-06 2.13E-06 mr1929 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