Search for Variation information by Variation ID:
Detailed information for vg0410563090:
| Variant ID: vg0410563090 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10563090 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CATACATTCATAGGTTATTCACATGAGGGACAACCTCACACACAAGGAATTTATCGCGGCTGTTCAAGAACAACTCATGGGATTCATCAACGAACAAGTC[C/A]
TTGATCCCGATGGTGAATTCTACTAAGACGGATCGACAATTCATAACATCGGTCCTTCTTCTTCTGAGATAACGCCGACGTTAAAGCCGTAGCTAGGACA
Reverse complement sequence
TGTCCTAGCTACGGCTTTAACGTCGGCGTTATCTCAGAAGAAGAAGGACCGATGTTATGAATTGTCGATCCGTCTTAGTAGAATTCACCATCGGGATCAA[G/T]
GACTTGTTCGTTGATGAATCCCATGAGTTGTTCTTGAACAGCCGCGATAAATTCCTTGTGTGTGAGGTTGTCCCTCATGTGAATAACCTATGAATGTATG
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 | 40.50% | 15.60% | 4.10% | 39.86% | NA |
| All Indica | 2759 | 10.00% | 18.40% | 5.22% | 66.36% | NA |
| All Japonica | 1512 | 99.10% | 0.30% | 0.07% | 0.53% | NA |
| Aus | 269 | 1.10% | 76.60% | 16.36% | 5.95% | NA |
| Indica I | 595 | 6.90% | 10.40% | 4.87% | 77.82% | NA |
| Indica II | 465 | 26.20% | 6.00% | 5.16% | 62.58% | NA |
| Indica III | 913 | 4.10% | 29.60% | 5.26% | 61.12% | NA |
| Indica Intermediate | 786 | 9.50% | 19.00% | 5.47% | 66.03% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 98.80% | 0.80% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 86.50% | 6.20% | 3.12% | 4.17% | NA |
| Intermediate | 90 | 58.90% | 11.10% | 2.22% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410563090 | C -> DEL | LOC_Os04g19000.1 | N | frameshift_variant | Average:10.943; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
| vg0410563090 | C -> A | LOC_Os04g19000.1 | missense_variant ; p.Leu558Ile; MODERATE | nonsynonymous_codon ; L558I | Average:10.943; most accessible tissue: Zhenshan97 root, score: 22.162 | benign  |
0.47 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0410563090 | 4.18E-06 | NA | mr1973 | 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 |
| vg0410563090 | NA | 3.70E-06 | mr1973 | 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 |