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Detailed information for vg0710993147:

Variant ID: vg0710993147 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 10993147
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGATTCCTTTAAATCAAAAAACAAGGAAGAATTTTCACCATGATGTACAGCTTCTCCAAGCATGGAAAACATTTAAGGAAGCCAAATTGTGTCCAGATTT[G/T]
GTCCAGCAGACTCAAGAACCAAAACCTTCACTGTGCGCAGCGAGGCTGTCGAACTGACGACCATCGTTTCCTGAAGAAAACCAAGACGTACAGCATGTCA

Reverse complement sequence

TGACATGCTGTACGTCTTGGTTTTCTTCAGGAAACGATGGTCGTCAGTTCGACAGCCTCGCTGCGCACAGTGAAGGTTTTGGTTCTTGAGTCTGCTGGAC[C/A]
AAATCTGGACACAATTTGGCTTCCTTAAATGTTTTCCATGCTTGGAGAAGCTGTACATCATGGTGAAAATTCTTCCTTGTTTTTTGATTTAAAGGAATCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.50% 9.40% 0.02% 0.00% NA
All Indica  2759 97.80% 2.10% 0.04% 0.00% NA
All Japonica  1512 80.40% 19.60% 0.00% 0.00% NA
Aus  269 95.20% 4.80% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 92.60% 7.30% 0.13% 0.00% NA
Temperate Japonica  767 66.90% 33.10% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 83.80% 16.20% 0.00% 0.00% NA
VI/Aromatic  96 22.90% 77.10% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0710993147 G -> T LOC_Os07g18600.1 missense_variant ; p.Pro332Gln; MODERATE nonsynonymous_codon ; P332Q Average:44.468; most accessible tissue: Zhenshan97 young leaf, score: 70.625 unknown unknown TOLERATED 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0710993147 NA 8.09E-26 Awn_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0710993147 NA 2.02E-09 mr1624 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
vg0710993147 NA 9.08E-09 mr1624_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
vg0710993147 NA 2.33E-06 mr1741_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
vg0710993147 NA 5.73E-06 mr1887_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