Search for Variation information by Variation ID:
Detailed information for vg1117780389:
| Variant ID: vg1117780389 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17780389 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 363. )
Flanking Sequence (100 bp) in Reference Genome:
TCTTCCTACATACCAAATTTCATTCCCGTACGAACTTGCTAAGTGTTTCATATGTAATGCATCCCACGCACATTGCAGATTCCACTGGGTGCTTTTACTC[T/A]
TCGACCTGGAGGCCTGCACCGTCAACGTATATGACTCAATGGATAAAAAAGAGTCTACGTTTGACAAGGTTTTCGAACTTATAGACAGGTACCGTCATAA
Reverse complement sequence
TTATGACGGTACCTGTCTATAAGTTCGAAAACCTTGTCAAACGTAGACTCTTTTTTATCCATTGAGTCATATACGTTGACGGTGCAGGCCTCCAGGTCGA[A/T]
GAGTAAAAGCACCCAGTGGAATCTGCAATGTGCGTGGGATGCATTACATATGAAACACTTAGCAAGTTCGTACGGGAATGAAATTTGGTATGTAGGAAGA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 25.00% | 0.10% | 1.31% | 73.57% | NA |
| All Indica | 2759 | 7.90% | 0.10% | 1.23% | 90.69% | NA |
| All Japonica | 1512 | 54.20% | 0.00% | 0.99% | 44.78% | NA |
| Aus | 269 | 9.30% | 0.00% | 2.97% | 87.73% | NA |
| Indica I | 595 | 6.10% | 0.00% | 0.17% | 93.78% | NA |
| Indica II | 465 | 23.20% | 0.00% | 1.72% | 75.05% | NA |
| Indica III | 913 | 1.80% | 0.40% | 1.20% | 96.60% | NA |
| Indica Intermediate | 786 | 7.50% | 0.00% | 1.78% | 90.71% | NA |
| Temperate Japonica | 767 | 63.20% | 0.00% | 1.69% | 35.07% | NA |
| Tropical Japonica | 504 | 27.60% | 0.00% | 0.40% | 72.02% | NA |
| Japonica Intermediate | 241 | 81.30% | 0.00% | 0.00% | 18.67% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 33.30% | 1.10% | 5.56% | 60.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117780389 | T -> A | LOC_Os11g30552.1 | missense_variant ; p.Phe1020Ile; MODERATE | nonsynonymous_codon ; F1020I | Average:5.943; most accessible tissue: Minghui63 young leaf, score: 9.976 | benign  |
0.551 |
TOLERATED | 0.36 |
| vg1117780389 | T -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:5.943; most accessible tissue: Minghui63 young leaf, score: 9.976 | N | N | N | N |