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Detailed information for vg0424200248:

Variant ID: vg0424200248 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 24200248
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCAACCGGAGAATTTTTGAATTAACCATACCGGCGTGAGATAGGTCTAGCAGCCGAAGTCGTGGGGCGTGGCCAACCACCAGCGGGTACTCATGCGACGT[C/T]
CATGGCCAGACGGCTATCGATAGCTCTGCCAGCTTCGGGAGCCACTCCAGCTCGATGGTGTAACAGGCGCAGAACTCGAGATCTATCGTGCTAAAGCTGC

Reverse complement sequence

GCAGCTTTAGCACGATAGATCTCGAGTTCTGCGCCTGTTACACCATCGAGCTGGAGTGGCTCCCGAAGCTGGCAGAGCTATCGATAGCCGTCTGGCCATG[G/A]
ACGTCGCATGAGTACCCGCTGGTGGTTGGCCACGCCCCACGACTTCGGCTGCTAGACCTATCTCACGCCGGTATGGTTAATTCAAAAATTCTCCGGTTGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.60% 0.70% 0.30% 1.38% NA
All Indica  2759 98.60% 0.00% 0.00% 1.45% NA
All Japonica  1512 97.00% 2.20% 0.86% 0.00% NA
Aus  269 90.70% 0.00% 0.37% 8.92% NA
Indica I  595 99.80% 0.00% 0.00% 0.17% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 96.60% 0.00% 0.00% 3.40% NA
Indica Intermediate  786 99.00% 0.00% 0.00% 1.02% NA
Temperate Japonica  767 96.10% 2.30% 1.56% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.20% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0424200248 C -> DEL LOC_Os04g40780.1 N frameshift_variant Average:71.556; most accessible tissue: Zhenshan97 panicle, score: 90.849 N N N N
vg0424200248 C -> T LOC_Os04g40780.1 stop_gained ; p.Trp202*; HIGH stop_gained Average:71.556; most accessible tissue: Zhenshan97 panicle, score: 90.849 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0424200248 NA 1.03E-06 Grain_weight Jap_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
vg0424200248 5.76E-06 5.76E-06 mr1191_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
vg0424200248 NA 8.23E-06 mr1827_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