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Detailed information for vg0712599200:

Variant ID: vg0712599200 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 12599200
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGTAGCTCAATCTTTCTCCAGTCAGGGAGATCAAAACAACCCCAGCTCCAGTGCCTGAAAGCCTCTTCGACCCATCAAAATGCATGGTCCAATACTCCAT[C/G]
TTCTCCTCGGGCATGTCTTCTTGGCACTCGGTCCACTTGGCGACAAAGTCGGCTAAAGCTTGGGACTTAATCGAAGTTCGTGGCTTGAAGGATATATCCA

Reverse complement sequence

TGGATATATCCTTCAAGCCACGAACTTCGATTAAGTCCCAAGCTTTAGCCGACTTTGTCGCCAAGTGGACCGAGTGCCAAGAAGACATGCCCGAGGAGAA[G/C]
ATGGAGTATTGGACCATGCATTTTGATGGGTCGAAGAGGCTTTCAGGCACTGGAGCTGGGGTTGTTTTGATCTCCCTGACTGGAGAAAGATTGAGCTACG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.60% 0.30% 0.23% 2.90% NA
All Indica  2759 99.90% 0.00% 0.00% 0.07% NA
All Japonica  1512 89.70% 0.70% 0.66% 8.93% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.00% 0.00% 0.25% NA
Temperate Japonica  767 80.30% 1.00% 1.17% 17.47% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.40% 0.41% 0.41% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 1.11% 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
vg0712599200 C -> DEL LOC_Os07g22420.1 N frameshift_variant Average:52.591; most accessible tissue: Minghui63 flag leaf, score: 82.521 N N N N
vg0712599200 C -> G LOC_Os07g22420.1 missense_variant ; p.Lys1100Asn; MODERATE nonsynonymous_codon ; K1100N Average:52.591; most accessible tissue: Minghui63 flag leaf, score: 82.521 benign 0.776 TOLERATED 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0712599200 2.78E-06 2.78E-06 mr1067 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