Search for Variation information by Variation ID:
Detailed information for vg1127979688:
| Variant ID: vg1127979688 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 27979688 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCTCCTGTGGGAGCTTAGTGATTCGCGTACCCTTGAGACCTAGGTACTTGAGCAGCCTGAGGCTCTCTAGCTGCTCACATATCTTCTTCAGGTGGGAGTC[C/A]
TCTATACCGATATTATCTTCAAGGTCCAACACTCGCAATCTTTTAAACATATCCAAGGGGACTCCTATCACGTCGCCAAGGATGACAAGGCTGCGAGTGT
Reverse complement sequence
ACACTCGCAGCCTTGTCATCCTTGGCGACGTGATAGGAGTCCCCTTGGATATGTTTAAAAGATTGCGAGTGTTGGACCTTGAAGATAATATCGGTATAGA[G/T]
GACTCCCACCTGAAGAAGATATGTGAGCAGCTAGAGAGCCTCAGGCTGCTCAAGTACCTAGGTCTCAAGGGTACGCGAATCACTAAGCTCCCACAGGAGA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.10% | 14.60% | 0.61% | 9.67% | NA |
| All Indica | 2759 | 72.30% | 19.20% | 0.62% | 7.94% | NA |
| All Japonica | 1512 | 77.20% | 8.50% | 0.66% | 13.56% | NA |
| Aus | 269 | 91.40% | 1.50% | 0.37% | 6.69% | NA |
| Indica I | 595 | 56.80% | 41.30% | 0.00% | 1.85% | NA |
| Indica II | 465 | 92.00% | 1.30% | 0.65% | 6.02% | NA |
| Indica III | 913 | 66.50% | 17.90% | 0.99% | 14.68% | NA |
| Indica Intermediate | 786 | 79.00% | 14.50% | 0.64% | 5.85% | NA |
| Temperate Japonica | 767 | 78.90% | 15.30% | 0.52% | 5.35% | NA |
| Tropical Japonica | 504 | 72.60% | 1.80% | 0.99% | 24.60% | NA |
| Japonica Intermediate | 241 | 81.70% | 1.20% | 0.41% | 16.60% | NA |
| VI/Aromatic | 96 | 64.60% | 25.00% | 0.00% | 10.42% | NA |
| Intermediate | 90 | 86.70% | 6.70% | 1.11% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1127979688 | C -> A | LOC_Os11g46200.1 | missense_variant ; p.Glu686Asp; MODERATE | nonsynonymous_codon ; E686D | Average:43.931; most accessible tissue: Callus, score: 81.053 | benign  |
-0.085 |
TOLERATED | 0.15 |
| vg1127979688 | C -> DEL | LOC_Os11g46200.1 | N | frameshift_variant | Average:43.931; most accessible tissue: Callus, score: 81.053 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1127979688 | 3.40E-06 | 3.40E-06 | mr1555 | Ind_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 |
| vg1127979688 | 3.70E-06 | 1.57E-06 | mr1640 | 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 |