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Detailed information for vg0717043053:

Variant ID: vg0717043053 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 17043053
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTCGTGTGGCACGTCTGGGGAATTGATATAGTTGAGATAGTCATCGAAGGTCTGTTTGAACCCTTTAATTTTCTTGGACGCACTTTTTGCTTTGTGCTT[G/C]
TGCGTCCTTACCATCACTGGCACATCGGCACCCTTAGATTCCTCTAGCTGCGATTGCTCTGGTTGCGATTGCTCTGGTTGATCGGGCATTGGCTGATCAA

Reverse complement sequence

TTGATCAGCCAATGCCCGATCAACCAGAGCAATCGCAACCAGAGCAATCGCAGCTAGAGGAATCTAAGGGTGCCGATGTGCCAGTGATGGTAAGGACGCA[C/G]
AAGCACAAAGCAAAAAGTGCGTCCAAGAAAATTAAAGGGTTCAAACAGACCTTCGATGACTATCTCAACTATATCAATTCCCCAGACGTGCCACACGAGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.10% 3.20% 1.76% 0.00% NA
All Indica  2759 99.10% 0.10% 0.80% 0.00% NA
All Japonica  1512 86.80% 9.40% 3.84% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 97.20% 0.00% 2.80% 0.00% NA
Temperate Japonica  767 94.10% 0.30% 5.61% 0.00% NA
Tropical Japonica  504 71.60% 26.60% 1.79% 0.00% NA
Japonica Intermediate  241 95.00% 2.50% 2.49% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 91.10% 6.70% 2.22% 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
vg0717043053 G -> C LOC_Os07g29080.1 missense_variant ; p.His372Gln; MODERATE nonsynonymous_codon ; H372Q Average:38.425; most accessible tissue: Zhenshan97 flag leaf, score: 53.795 unknown unknown TOLERATED 0.14

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0717043053 3.51E-06 NA mr1055 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
vg0717043053 8.78E-06 NA mr1390 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
vg0717043053 6.90E-06 NA mr1490 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
vg0717043053 7.33E-06 NA mr1178_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
vg0717043053 2.15E-06 NA mr1390_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
vg0717043053 3.83E-07 NA mr1490_2 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