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Detailed information for vg0307808360:

Variant ID: vg0307808360 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 7808360
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACAAGATTCTTCTTTATTGAAGGGACATGCTGCACGTTCTTCAGCTGCACGGTATTTCCCGAAGTAAACTTCAGATCGACCGTACCAACACCATGAACA[G/A]
CCGCAAGCGACCCGTTTCCCATCAACAAGGAGGAACCTCTCCCAACCTGATAAGAAGAAAACAGAGAAATGTCAGCATATACATGAATATTAGCACCAGT

Reverse complement sequence

ACTGGTGCTAATATTCATGTATATGCTGACATTTCTCTGTTTTCTTCTTATCAGGTTGGGAGAGGTTCCTCCTTGTTGATGGGAAACGGGTCGCTTGCGG[C/T]
TGTTCATGGTGTTGGTACGGTCGATCTGAAGTTTACTTCGGGAAATACCGTGCAGCTGAAGAACGTGCAGCATGTCCCTTCAATAAAGAAGAATCTTGTT

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 31.90% 0.70% 34.98% 32.44% NA
All Indica  2759 6.50% 1.10% 38.96% 53.50% NA
All Japonica  1512 85.10% 0.10% 14.02% 0.73% NA
Aus  269 1.10% 0.00% 97.03% 1.86% NA
Indica I  595 9.40% 0.30% 20.50% 69.75% NA
Indica II  465 2.20% 0.20% 24.52% 73.12% NA
Indica III  913 3.10% 1.60% 57.61% 37.68% NA
Indica Intermediate  786 10.70% 1.50% 39.82% 47.96% NA
Temperate Japonica  767 98.00% 0.00% 1.30% 0.65% NA
Tropical Japonica  504 65.30% 0.40% 33.73% 0.60% NA
Japonica Intermediate  241 85.50% 0.00% 13.28% 1.24% NA
VI/Aromatic  96 5.20% 2.10% 82.29% 10.42% NA
Intermediate  90 36.70% 0.00% 28.89% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0307808360 G -> A LOC_Os03g14349.1 missense_variant ; p.Ala450Val; MODERATE nonsynonymous_codon ; A450I Average:15.971; most accessible tissue: Minghui63 root, score: 25.504 possibly damaging 1.638 DELETERIOUS 0.00
vg0307808360 G -> A LOC_Os03g14349.1 missense_variant ; p.Ala450Val; MODERATE nonsynonymous_codon ; A450V Average:15.971; most accessible tissue: Minghui63 root, score: 25.504 benign 0.593 TOLERATED 0.09
vg0307808360 G -> DEL LOC_Os03g14349.1 N frameshift_variant Average:15.971; most accessible tissue: Minghui63 root, score: 25.504 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0307808360 NA 2.96E-06 mr1568 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
vg0307808360 4.06E-06 1.19E-10 mr1690_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