Search for Variation information by Variation ID:
Detailed information for vg1114410670:
| Variant ID: vg1114410670 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 14410670 |
| Reference Allele: GA | Alternative Allele: AA,G |
| Primary Allele: GA | Secondary Allele: AA |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGGGAAATAAAATCCTACTCTTCAAAAACGGGGAGAACAGACTACCCCAAGTCACCGAATTCGTCCATCACGCCCTTGCGCGTGTCATTGGCGGCCCCCT[GA/AA,G]
TCCAAGATCCTCTGGAGGTCGATATTAGGGTGCGCCAACCTCATGCACGCGAGGACGTGGCTCGCCCCGGTGTAGATCCCGTTAAACATCTCCTCGCCGA
Reverse complement sequence
TCGGCGAGGAGATGTTTAACGGGATCTACACCGGGGCGAGCCACGTCCTCGCGTGCATGAGGTTGGCGCACCCTAATATCGACCTCCAGAGGATCTTGGA[TC/TT,C]
AGGGGGCCGCCAATGACACGCGCAAGGGCGTGATGGACGAATTCGGTGACTTGGGGTAGTCTGTTCTCCCCGTTTTTGAAGAGTAGGATTTTATTTCCCC
Allele Frequencies:
| Populations | Population Size | Frequency of GA(primary allele) | Frequency of AA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.80% | 0.80% | 7.68% | 9.50% | G: 0.25% |
| All Indica | 2759 | 77.00% | 1.40% | 12.72% | 8.55% | G: 0.36% |
| All Japonica | 1512 | 87.90% | 0.00% | 0.53% | 11.57% | NA |
| Aus | 269 | 92.60% | 0.00% | 0.37% | 6.69% | G: 0.37% |
| Indica I | 595 | 75.00% | 1.00% | 14.79% | 9.08% | G: 0.17% |
| Indica II | 465 | 86.70% | 0.40% | 7.31% | 5.59% | NA |
| Indica III | 913 | 68.10% | 2.40% | 17.31% | 11.39% | G: 0.77% |
| Indica Intermediate | 786 | 83.10% | 1.00% | 9.03% | 6.62% | G: 0.25% |
| Temperate Japonica | 767 | 86.30% | 0.00% | 0.52% | 13.17% | NA |
| Tropical Japonica | 504 | 94.60% | 0.00% | 0.00% | 5.36% | NA |
| Japonica Intermediate | 241 | 78.80% | 0.00% | 1.66% | 19.50% | NA |
| VI/Aromatic | 96 | 82.30% | 0.00% | 1.04% | 16.67% | NA |
| Intermediate | 90 | 92.20% | 0.00% | 2.22% | 4.44% | G: 1.11% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114410670 | GA -> AA | LOC_Os11g25290.1 | stop_gained ; p.Gln456*; HIGH | stop_gained | Average:31.521; most accessible tissue: Zhenshan97 root, score: 47.644 | N | N | N | N |
| vg1114410670 | GA -> AA | LOC_Os11g25290.1 | stop_gained ; p.Gln456*; HIGH | nonsynonymous_codon ; Q456Y | Average:31.521; most accessible tissue: Zhenshan97 root, score: 47.644 | possibly damaging  |
+1.920 |
N | N |
| vg1114410670 | GA -> DEL | LOC_Os11g25290.1 | N | frameshift_variant | Average:31.521; most accessible tissue: Zhenshan97 root, score: 47.644 | N | N | N | N |
| vg1114410670 | GA -> G | LOC_Os11g25290.1 | frameshift_variant ; p.Gln456fs; HIGH | frameshift_variant | Average:31.521; most accessible tissue: Zhenshan97 root, score: 47.644 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1114410670 | 9.44E-07 | 1.28E-06 | mr1240_2 | 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 |
| vg1114410670 | NA | 7.35E-07 | mr1496_2 | Ind_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 |