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Detailed information for vg1004721834:

Variant ID: vg1004721834 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4721834
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTCCGTACGAAGCACTGTATGGTCGGAAGTGCCGCACTCCGCTTTTGTGGGATCAAACGGGAGAACGTCAGGTTTTCGGGAAGCAGAAGAGAAGGTAAA[G/C]
ATCATTCAAGAAAGGTTGCGTGTGGCTCAGTCTCGCCATAAGAGTTATGCCGACAATCGCCGCAGAGATTTGAGTTTTGAAGAAGGAGATTATGTGTACC

Reverse complement sequence

GGTACACATAATCTCCTTCTTCAAAACTCAAATCTCTGCGGCGATTGTCGGCATAACTCTTATGGCGAGACTGAGCCACACGCAACCTTTCTTGAATGAT[C/G]
TTTACCTTCTCTTCTGCTTCCCGAAAACCTGACGTTCTCCCGTTTGATCCCACAAAAGCGGAGTGCGGCACTTCCGACCATACAGTGCTTCGTACGGAGC

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 86.60% 2.30% 1.54% 9.54% NA
All Indica  2759 91.70% 0.30% 1.41% 6.63% NA
All Japonica  1512 87.80% 6.50% 0.20% 5.49% NA
Aus  269 23.80% 0.00% 11.15% 65.06% NA
Indica I  595 80.30% 0.00% 0.50% 19.16% NA
Indica II  465 94.40% 0.00% 0.43% 5.16% NA
Indica III  913 95.50% 0.90% 2.19% 1.42% NA
Indica Intermediate  786 94.10% 0.00% 1.78% 4.07% NA
Temperate Japonica  767 95.20% 0.10% 0.00% 4.69% NA
Tropical Japonica  504 79.80% 19.00% 0.00% 1.19% NA
Japonica Intermediate  241 80.90% 0.80% 1.24% 17.01% NA
VI/Aromatic  96 95.80% 0.00% 1.04% 3.12% NA
Intermediate  90 88.90% 3.30% 0.00% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1004721834 G -> C LOC_Os10g08702.1 missense_variant ; p.Lys1101Asn; MODERATE nonsynonymous_codon ; K1101N Average:12.562; most accessible tissue: Minghui63 young leaf, score: 32.638 possibly damaging 1.918 DELETERIOUS 0.00
vg1004721834 G -> DEL LOC_Os10g08702.1 N frameshift_variant Average:12.562; most accessible tissue: Minghui63 young leaf, score: 32.638 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004721834 2.83E-06 NA mr1817 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