Search for Variation information by Variation ID:
Detailed information for vg0614961730:
| Variant ID: vg0614961730 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 14961730 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 386. )
Flanking Sequence (100 bp) in Reference Genome:
AACACCATCGGCAGGATGGTGAGCCAGTAAGCCTGGTCGCGTGTGCACAAGGACGAAAGTCCTAGCGGTGCTCTCGCAGCGACGGCCTCTTCTGTGTACG[G/T]
CTCCCAGATGACGTCGCTCGGCTGGAGACGGTCAAACTCGAACACGAAGTCCGGGTAACCACGTCTCACCTGGACGTGAGCGTAACGACGCTGCAATAAA
Reverse complement sequence
TTTATTGCAGCGTCGTTACGCTCACGTCCAGGTGAGACGTGGTTACCCGGACTTCGTGTTCGAGTTTGACCGTCTCCAGCCGAGCGACGTCATCTGGGAG[C/A]
CGTACACAGAAGAGGCCGTCGCTGCGAGAGCACCGCTAGGACTTTCGTCCTTGTGCACACGCGACCAGGCTTACTGGCTCACCATCCTGCCGATGGTGTT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.60% | 0.10% | 28.86% | 32.44% | NA |
| All Indica | 2759 | 25.40% | 0.20% | 25.41% | 48.97% | NA |
| All Japonica | 1512 | 55.60% | 0.00% | 38.03% | 6.35% | NA |
| Aus | 269 | 65.10% | 0.00% | 17.10% | 17.84% | NA |
| Indica I | 595 | 17.10% | 0.20% | 31.93% | 50.76% | NA |
| Indica II | 465 | 26.00% | 0.40% | 24.30% | 49.25% | NA |
| Indica III | 913 | 30.60% | 0.00% | 19.17% | 50.27% | NA |
| Indica Intermediate | 786 | 25.30% | 0.40% | 28.37% | 45.93% | NA |
| Temperate Japonica | 767 | 46.50% | 0.00% | 50.07% | 3.39% | NA |
| Tropical Japonica | 504 | 63.30% | 0.00% | 25.20% | 11.51% | NA |
| Japonica Intermediate | 241 | 68.50% | 0.00% | 26.56% | 4.98% | NA |
| VI/Aromatic | 96 | 68.80% | 0.00% | 14.58% | 16.67% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 31.11% | 24.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0614961730 | G -> T | LOC_Os06g25580.1 | missense_variant ; p.Pro1178Thr; MODERATE | nonsynonymous_codon ; P1178R | Average:5.437; most accessible tissue: Callus, score: 15.135 | probably damaging  |
2.379 |
DELETERIOUS | 0.00 |
| vg0614961730 | G -> DEL | LOC_Os06g25580.1 | N | frameshift_variant | Average:5.437; most accessible tissue: Callus, score: 15.135 | N | N | N | N |