Search for Variation information by Variation ID:
Detailed information for vg1208920255:
| Variant ID: vg1208920255 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8920255 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCCTGTCTTCGTTGTTCCCAAAGAACAGCCGGACAAGATTTTGTCTTGGACCACAAAGCCCTCCTTGAACCCCTCTCTTCAGTCGTTTATCGACATCATC[A/G]
ACGATCTGCGAGTACGGGGCTTGTCGGGGTATGAAGTCGTTGCAGACTTCGTTGGTAGGCGGATCCAGCCACTCTAGGCTCGGGCCCATCCAGCCTTTAA
Reverse complement sequence
TTAAAGGCTGGATGGGCCCGAGCCTAGAGTGGCTGGATCCGCCTACCAACGAAGTCTGCAACGACTTCATACCCCGACAAGCCCCGTACTCGCAGATCGT[T/C]
GATGATGTCGATAAACGACTGAAGAGAGGGGTTCAAGGAGGGCTTTGTGGTCCAAGACAAAATCTTGTCCGGCTGTTCTTTGGGAACAACGAAGACAGGG
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 | 76.60% | 5.60% | 4.70% | 13.14% | NA |
| All Indica | 2759 | 62.10% | 9.30% | 7.68% | 20.91% | NA |
| All Japonica | 1512 | 98.70% | 0.10% | 0.13% | 0.99% | NA |
| Aus | 269 | 88.50% | 0.70% | 2.60% | 8.18% | NA |
| Indica I | 595 | 47.60% | 13.90% | 8.40% | 30.08% | NA |
| Indica II | 465 | 60.40% | 6.20% | 13.76% | 19.57% | NA |
| Indica III | 913 | 70.40% | 7.90% | 3.50% | 18.18% | NA |
| Indica Intermediate | 786 | 64.50% | 9.20% | 8.40% | 17.94% | NA |
| Temperate Japonica | 767 | 98.80% | 0.10% | 0.26% | 0.78% | NA |
| Tropical Japonica | 504 | 98.80% | 0.20% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 91.10% | 3.30% | 1.11% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208920255 | A -> DEL | LOC_Os12g15620.1 | N | frameshift_variant | Average:34.368; most accessible tissue: Minghui63 young leaf, score: 73.49 | N | N | N | N |
| vg1208920255 | A -> G | LOC_Os12g15620.1 | missense_variant ; p.Asn194Asp; MODERATE | nonsynonymous_codon | Average:34.368; most accessible tissue: Minghui63 young leaf, score: 73.49 | benign  |
-0.777 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208920255 | NA | 3.53E-09 | mr1707_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 |