Search for Variation information by Variation ID:
Detailed information for vg1008173119:
| Variant ID: vg1008173119 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 8173119 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CACCGCAGCCCCACCATCGACCATCATCTTAGACATCGGCTTCCCATTGACAAAACCATTTACATACAATGGCTTAAGATGCCGATTCTCTGTCCCTTCT[G/A]
GTTTCTCAAAGACTGCTTGTTCTGGTGATAAAATCAACTTAGCCGATTCCTCCTCCACTTCATCAACATCGGCTTGCTTGATTCCAAATTCCGCAGGTAG
Reverse complement sequence
CTACCTGCGGAATTTGGAATCAAGCAAGCCGATGTTGATGAAGTGGAGGAGGAATCGGCTAAGTTGATTTTATCACCAGAACAAGCAGTCTTTGAGAAAC[C/T]
AGAAGGGACAGAGAATCGGCATCTTAAGCCATTGTATGTAAATGGTTTTGTCAATGGGAAGCCGATGTCTAAGATGATGGTCGATGGTGGGGCTGCGGTG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 42.20% | 27.50% | 10.77% | 19.53% | NA |
| All Indica | 2759 | 63.60% | 9.80% | 13.56% | 13.08% | NA |
| All Japonica | 1512 | 11.20% | 52.60% | 4.96% | 31.22% | NA |
| Aus | 269 | 4.10% | 46.80% | 21.19% | 27.88% | NA |
| Indica I | 595 | 94.60% | 1.00% | 2.69% | 1.68% | NA |
| Indica II | 465 | 64.30% | 6.00% | 15.27% | 14.41% | NA |
| Indica III | 913 | 43.20% | 18.40% | 18.84% | 19.61% | NA |
| Indica Intermediate | 786 | 63.40% | 8.70% | 14.63% | 13.36% | NA |
| Temperate Japonica | 767 | 2.50% | 45.00% | 6.91% | 45.63% | NA |
| Tropical Japonica | 504 | 26.80% | 55.80% | 2.18% | 15.28% | NA |
| Japonica Intermediate | 241 | 6.60% | 70.10% | 4.56% | 18.67% | NA |
| VI/Aromatic | 96 | 27.10% | 70.80% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 37.80% | 44.40% | 2.22% | 15.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1008173119 | G -> A | LOC_Os10g16390.1 | missense_variant ; p.Pro403Leu; MODERATE | nonsynonymous_codon ; P403L | Average:22.184; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 | benign  |
0.64 |
TOLERATED | 0.07 |
| vg1008173119 | G -> DEL | LOC_Os10g16390.1 | N | frameshift_variant | Average:22.184; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1008173119 | NA | 9.84E-07 | mr1495 | 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 |
| vg1008173119 | NA | 7.01E-10 | mr1945 | 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 |