Search for Variation information by Variation ID:
Detailed information for vg0819980575:
| Variant ID: vg0819980575 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 19980575 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTCGTATTGACCGTACTGAGGCCGAATTAACCCCCCTTGCTGATAATGGGCTTGCGGAGAAGGAGGTTGATATTGATAATTTAAATTGCCCCCCTGGTAA[T/C]
TTTGGTAGTTTGGCTGAATATTTCGCACCAAGTGCTCAGGGACAATCTAAGGTACTACCGTGTGGTCCGGCTGCACGTGATGGACCAAATGCTCTGGGAC
Reverse complement sequence
GTCCCAGAGCATTTGGTCCATCACGTGCAGCCGGACCACACGGTAGTACCTTAGATTGTCCCTGAGCACTTGGTGCGAAATATTCAGCCAAACTACCAAA[A/G]
TTACCAGGGGGGCAATTTAAATTATCAATATCAACCTCCTTCTCCGCAAGCCCATTATCAGCAAGGGGGGTTAATTCGGCCTCAGTACGGTCAATACGAG
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 | 36.00% | 0.10% | 1.78% | 62.04% | NA |
| All Indica | 2759 | 9.10% | 0.20% | 2.61% | 88.08% | NA |
| All Japonica | 1512 | 90.90% | 0.10% | 0.13% | 8.86% | NA |
| Aus | 269 | 2.60% | 0.00% | 1.86% | 95.54% | NA |
| Indica I | 595 | 10.80% | 0.00% | 1.01% | 88.24% | NA |
| Indica II | 465 | 10.80% | 0.00% | 5.59% | 83.66% | NA |
| Indica III | 913 | 5.50% | 0.70% | 2.30% | 91.57% | NA |
| Indica Intermediate | 786 | 11.10% | 0.00% | 2.42% | 86.51% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 79.40% | 0.20% | 0.40% | 20.04% | NA |
| Japonica Intermediate | 241 | 88.80% | 0.00% | 0.00% | 11.20% | NA |
| VI/Aromatic | 96 | 29.20% | 0.00% | 4.17% | 66.67% | NA |
| Intermediate | 90 | 46.70% | 0.00% | 1.11% | 52.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0819980575 | T -> C | LOC_Os08g32250.1 | missense_variant ; p.Asn130Ser; MODERATE | nonsynonymous_codon | Average:10.894; most accessible tissue: Callus, score: 43.556 | benign  |
1.207 |
TOLERATED | 0.13 |
| vg0819980575 | T -> DEL | LOC_Os08g32250.1 | N | frameshift_variant | Average:10.894; most accessible tissue: Callus, score: 43.556 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0819980575 | 2.58E-06 | NA | mr1336 | 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 |