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Detailed information for vg0902470420:

Variant ID: vg0902470420 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 2470420
Reference Allele: CAlternative Allele: T,A
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACAAATTACTTTTATGATATGTCTAAATTACTTTTAGATTTCACTAAGTTACTTCTTAGACATATAAAAGTAAATTTAGTAAAGCCTAAAAGTAATTTA[C/T,A]
ATATATTATAGAAGTAACTTATAACAAAAGGAAAGTAACTTTAATTAATGTCTTTTTTCATTGAACAAATTATCATATATATAATTTACTTCTAGATTTG

Reverse complement sequence

CAAATCTAGAAGTAAATTATATATATGATAATTTGTTCAATGAAAAAAGACATTAATTAAAGTTACTTTCCTTTTGTTATAAGTTACTTCTATAATATAT[G/A,T]
TAAATTACTTTTAGGCTTTACTAAATTTACTTTTATATGTCTAAGAAGTAACTTAGTGAAATCTAAAAGTAATTTAGACATATCATAAAAGTAATTTGTG

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 92.60% 7.40% 0.02% 0.00% NA
All Indica  2759 95.40% 4.60% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 19.00% 81.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 92.90% 6.90% 0.22% 0.00% NA
Indica III  913 96.20% 3.80% 0.00% 0.00% NA
Indica Intermediate  786 92.50% 7.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0902470420 C -> T LOC_Os09g04624.1 intron_variant ; MODIFIER silent_mutation Average:20.574; most accessible tissue: Zhenshan97 root, score: 29.203 N N N N
vg0902470420 C -> T LOC_Os09g04624.2 intron_variant ; MODIFIER silent_mutation Average:20.574; most accessible tissue: Zhenshan97 root, score: 29.203 N N N N
vg0902470420 C -> A LOC_Os09g04624.1 intron_variant ; MODIFIER N Average:20.574; most accessible tissue: Zhenshan97 root, score: 29.203 N N N N
vg0902470420 C -> A LOC_Os09g04624.2 intron_variant ; MODIFIER N Average:20.574; most accessible tissue: Zhenshan97 root, score: 29.203 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0902470420 NA 7.87E-06 mr1230 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
vg0902470420 NA 1.66E-07 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
vg0902470420 2.80E-07 NA mr1208_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