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Detailed information for vg0714165066:

Variant ID: vg0714165066 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 14165066
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCACGATCACTAGTCAACGTCACGCGAACACGACACTTCTCCTCGTTGGGGTCATGGGGAATCTGGCGATACTCGGGGGCAACCTCGTAACCTACTTCA[A/G]
ATGCCATCATTCTCAGCTCCCTGACGAATCCTAGCACCTCGATCAAGTTTTTCGGCGGATGGGCATCTAAAGCAACATGGAAAGGAAGGAATTAATGCAT

Reverse complement sequence

ATGCATTAATTCCTTCCTTTCCATGTTGCTTTAGATGCCCATCCGCCGAAAAACTTGATCGAGGTGCTAGGATTCGTCAGGGAGCTGAGAATGATGGCAT[T/C]
TGAAGTAGGTTACGAGGTTGCCCCCGAGTATCGCCAGATTCCCCATGACCCCAACGAGGAGAAGTGTCGTGTTCGCGTGACGTTGACTAGTGATCGTGAA

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 41.30% 36.40% 11.11% 11.17% NA
All Indica  2759 57.00% 26.90% 14.35% 1.81% NA
All Japonica  1512 8.60% 58.60% 5.56% 27.25% NA
Aus  269 70.60% 18.60% 9.67% 1.12% NA
Indica I  595 33.10% 47.70% 16.13% 3.03% NA
Indica II  465 57.20% 27.50% 13.98% 1.29% NA
Indica III  913 79.60% 8.10% 10.95% 1.31% NA
Indica Intermediate  786 48.60% 32.40% 17.18% 1.78% NA
Temperate Japonica  767 0.40% 74.10% 2.22% 23.34% NA
Tropical Japonica  504 22.00% 38.90% 9.72% 29.37% NA
Japonica Intermediate  241 6.60% 50.60% 7.47% 35.27% NA
VI/Aromatic  96 30.20% 6.20% 7.29% 56.25% NA
Intermediate  90 33.30% 43.30% 13.33% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0714165066 A -> DEL LOC_Os07g24910.1 N frameshift_variant Average:11.635; most accessible tissue: Callus, score: 35.383 N N N N
vg0714165066 A -> G LOC_Os07g24910.1 missense_variant ; p.Phe4Ser; MODERATE nonsynonymous_codon ; F4P Average:11.635; most accessible tissue: Callus, score: 35.383 probably damaging 2.332 DELETERIOUS 0.00
vg0714165066 A -> G LOC_Os07g24910.1 missense_variant ; p.Phe4Ser; MODERATE nonsynonymous_codon ; F4S Average:11.635; most accessible tissue: Callus, score: 35.383 possibly damaging 1.71 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0714165066 NA 4.24E-08 mr1695 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
vg0714165066 6.09E-06 6.09E-06 mr1726 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