Search for Variation information by Variation ID:
Detailed information for vg1121947030:
| Variant ID: vg1121947030 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21947030 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 236. )
Flanking Sequence (100 bp) in Reference Genome:
GATCATGGTCAAGAAGATGAAGGGACTAGGAAGAATCAATGGTGTCCCTCTGGTATTTACACAAAAAATCAGAAAAGGAGGGTCCAGAGATTGAGGAGCA[G/T]
GGAACGTTTTCAAGAGGTTGAAGAGGGAATCAATCATCGGCTGAGGAAACCAAGACCAAGGCAGGTGTGGCGTGTTAAGAATCAAGCTCCTACAGCCGAT
Reverse complement sequence
ATCGGCTGTAGGAGCTTGATTCTTAACACGCCACACCTGCCTTGGTCTTGGTTTCCTCAGCCGATGATTGATTCCCTCTTCAACCTCTTGAAAACGTTCC[C/A]
TGCTCCTCAATCTCTGGACCCTCCTTTTCTGATTTTTTGTGTAAATACCAGAGGGACACCATTGATTCTTCCTAGTCCCTTCATCTTCTTGACCATGATC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.50% | 7.80% | 0.85% | 3.83% | NA |
| All Indica | 2759 | 95.70% | 0.70% | 0.83% | 2.79% | NA |
| All Japonica | 1512 | 79.90% | 17.90% | 0.33% | 1.92% | NA |
| Aus | 269 | 75.80% | 0.40% | 3.72% | 20.07% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 99.10% | 0.40% | 0.00% | 0.43% | NA |
| Indica III | 913 | 92.00% | 1.20% | 2.08% | 4.71% | NA |
| Indica Intermediate | 786 | 94.70% | 0.90% | 0.51% | 3.94% | NA |
| Temperate Japonica | 767 | 92.00% | 7.80% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 57.50% | 37.30% | 0.40% | 4.76% | NA |
| Japonica Intermediate | 241 | 88.00% | 9.10% | 1.24% | 1.66% | NA |
| VI/Aromatic | 96 | 14.60% | 67.70% | 2.08% | 15.62% | NA |
| Intermediate | 90 | 77.80% | 15.60% | 0.00% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1121947030 | G -> T | LOC_Os11g37170.1 | missense_variant ; p.Arg656Met; MODERATE | nonsynonymous_codon ; R656M | Average:37.02; most accessible tissue: Minghui63 young leaf, score: 48.378 | probably damaging  |
2.58 |
TOLERATED | 0.08 |
| vg1121947030 | G -> DEL | LOC_Os11g37170.1 | N | frameshift_variant | Average:37.02; most accessible tissue: Minghui63 young leaf, score: 48.378 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121947030 | NA | 1.20E-06 | mr1045 | 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 |
| vg1121947030 | NA | 5.51E-06 | mr1215 | 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 |
| vg1121947030 | NA | 1.97E-09 | mr1278 | 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 |
| vg1121947030 | NA | 2.30E-09 | mr1442 | 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 |
| vg1121947030 | NA | 5.57E-06 | mr1470 | 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 |
| vg1121947030 | 3.53E-06 | 3.52E-06 | mr1481 | 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 |
| vg1121947030 | NA | 8.48E-06 | mr1596 | 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 |
| vg1121947030 | 5.48E-06 | NA | mr1629 | 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 |
| vg1121947030 | NA | 6.71E-07 | mr1629 | 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 |
| vg1121947030 | NA | 1.15E-06 | mr1982 | 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 |