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Detailed information for vg0609473231:

Variant ID: vg0609473231 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9473231
Reference Allele: GAlternative Allele: A,C
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGGGCATCTGACAATCTTCCACCAACTTACTAAACTTCTCAAAATCTCTGTCGTTGTCCTCTGCGTCTTCAATGTTATGCAACATTGTAGATAGACATT[G/A,C]
AGTGTCCAAATCTATGGTATCTCCACCTAACGGAGAAGGTACGAACATGCCTTCTCGAGCTGCGGCGGTGTTCTCTACATCCTGATCCAACACTTCTTCA

Reverse complement sequence

TGAAGAAGTGTTGGATCAGGATGTAGAGAACACCGCCGCAGCTCGAGAAGGCATGTTCGTACCTTCTCCGTTAGGTGGAGATACCATAGATTTGGACACT[C/T,G]
AATGTCTATCTACAATGTTGCATAACATTGAAGACGCAGAGGACAACGACAGAGATTTTGAGAAGTTTAGTAAGTTGGTGGAAGATTGTCAGATGCCCTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 68.80% 19.70% 10.88% 0.66% NA
All Indica  2759 94.20% 2.50% 3.37% 0.00% NA
All Japonica  1512 33.50% 43.70% 20.77% 2.05% NA
Aus  269 23.00% 45.40% 31.60% 0.00% NA
Indica I  595 91.40% 2.00% 6.55% 0.00% NA
Indica II  465 96.60% 0.40% 3.01% 0.00% NA
Indica III  913 95.00% 3.90% 1.10% 0.00% NA
Indica Intermediate  786 93.90% 2.30% 3.82% 0.00% NA
Temperate Japonica  767 52.90% 21.40% 21.90% 3.78% NA
Tropical Japonica  504 12.90% 72.00% 15.08% 0.00% NA
Japonica Intermediate  241 14.50% 55.60% 29.05% 0.83% NA
VI/Aromatic  96 21.90% 62.50% 15.62% 0.00% NA
Intermediate  90 71.10% 21.10% 7.78% 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
vg0609473231 G -> C LOC_Os06g16510.1 missense_variant ; p.Gln71Glu; MODERATE N Average:30.945; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 N N N N
vg0609473231 G -> A LOC_Os06g16510.1 stop_gained ; p.Gln71*; HIGH stop_gained Average:30.945; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 N N N N
vg0609473231 G -> DEL LOC_Os06g16510.1 N frameshift_variant Average:30.945; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609473231 NA 2.46E-09 mr1666 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
vg0609473231 NA 3.04E-07 mr1570_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