Search for Variation information by Variation ID:
Detailed information for vg0627801383:
| Variant ID: vg0627801383 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 27801383 |
| 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: 263. )
Flanking Sequence (100 bp) in Reference Genome:
TTACAAGGTTTTGATATGGATGCATGACATACAGGCTGATTATTACAATAAAACCGGATGCTTTAACTTGGACTGTGACGGTTTTGTACCAGTAAACGGT[G/T]
CCCCGGTGACTCCTGGAGATACATTAGAACAAGCTAATAACCAAACTAAAATATCATTCAAGATATTTAAGGTAATGTAACTAATAATTATTTGATCCTA
Reverse complement sequence
TAGGATCAAATAATTATTAGTTACATTACCTTAAATATCTTGAATGATATTTTAGTTTGGTTATTAGCTTGTTCTAATGTATCTCCAGGAGTCACCGGGG[C/A]
ACCGTTTACTGGTACAAAACCGTCACAGTCCAAGTTAAAGCATCCGGTTTTATTGTAATAATCAGCCTGTATGTCATGCATCCATATCAAAACCTTGTAA
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 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.20% | 4.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0627801383 | G -> T | LOC_Os06g45920.1 | missense_variant ; p.Ala94Ser; MODERATE | nonsynonymous_codon ; A94S | Average:47.077; most accessible tissue: Minghui63 panicle, score: 59.629 | possibly damaging  |
1.661 |
TOLERATED | 0.30 |