Search for Variation information by Variation ID:
Detailed information for vg0400034660:
| Variant ID: vg0400034660 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 34660 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.20, others allele: 0.00, population size: 55. )
Flanking Sequence (100 bp) in Reference Genome:
AAATTGCCGCAACCAACAGGGGGCTAACCAAAGGATCCGCTACACCAATCCCTATCCAGGGGGATCCTCCTCGCAGCAGCAGCAACAGCAGCAGCAACCA[T/C]
GCTCCGCGCCCCGACCTCAATTTGTGGTGCGCGTCCCACAGCCGCAGCAACAGCAGAGTCAACAAGGGACTCGTGCGCCCCGTCCTCCTACGCCAGCCGT
Reverse complement sequence
ACGGCTGGCGTAGGAGGACGGGGCGCACGAGTCCCTTGTTGACTCTGCTGTTGCTGCGGCTGTGGGACGCGCACCACAAATTGAGGTCGGGGCGCGGAGC[A/G]
TGGTTGCTGCTGCTGTTGCTGCTGCTGCGAGGAGGATCCCCCTGGATAGGGATTGGTGTAGCGGATCCTTTGGTTAGCCCCCTGTTGGTTGCGGCAATTT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.60% | 4.10% | 22.96% | 53.32% | NA |
| All Indica | 2759 | 5.50% | 1.20% | 21.38% | 71.95% | NA |
| All Japonica | 1512 | 47.80% | 9.20% | 10.38% | 32.61% | NA |
| Aus | 269 | 9.70% | 4.80% | 85.13% | 0.37% | NA |
| Indica I | 595 | 6.70% | 0.00% | 16.64% | 76.64% | NA |
| Indica II | 465 | 6.70% | 0.60% | 11.40% | 81.29% | NA |
| Indica III | 913 | 2.70% | 2.80% | 28.15% | 66.27% | NA |
| Indica Intermediate | 786 | 7.00% | 0.50% | 23.03% | 69.47% | NA |
| Temperate Japonica | 767 | 72.20% | 15.60% | 1.69% | 10.43% | NA |
| Tropical Japonica | 504 | 17.30% | 2.40% | 24.60% | 55.75% | NA |
| Japonica Intermediate | 241 | 34.00% | 2.90% | 8.30% | 54.77% | NA |
| VI/Aromatic | 96 | 3.10% | 6.20% | 84.38% | 6.25% | NA |
| Intermediate | 90 | 25.60% | 4.40% | 31.11% | 38.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0400034660 | T -> C | LOC_Os04g01040.1 | missense_variant ; p.Cys590Arg; MODERATE | nonsynonymous_codon ; C590R | Average:33.009; most accessible tissue: Minghui63 young leaf, score: 51.901 | probably damaging  |
-2.729 |
TOLERATED | 1.00 |
| vg0400034660 | T -> DEL | LOC_Os04g01040.1 | N | frameshift_variant | Average:33.009; most accessible tissue: Minghui63 young leaf, score: 51.901 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0400034660 | 1.97E-06 | 1.97E-06 | mr1166_2 | 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 |
| vg0400034660 | 1.06E-06 | NA | mr1305_2 | 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 |
| vg0400034660 | 4.65E-08 | 2.39E-08 | mr1305_2 | 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 |
| vg0400034660 | NA | 3.42E-06 | mr1409_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 |
| vg0400034660 | 6.11E-06 | 3.25E-06 | mr1559_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 |
| vg0400034660 | 3.09E-07 | 7.53E-07 | mr1585_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 |
| vg0400034660 | 3.53E-06 | NA | mr1670_2 | 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 |
| vg0400034660 | 4.65E-08 | 4.65E-08 | mr1670_2 | 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 |
| vg0400034660 | 6.69E-07 | 2.13E-07 | mr1765_2 | 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 |