Search for Variation information by Variation ID:
Detailed information for vg1105974479:
| Variant ID: vg1105974479 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974479 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTC[G/A]
CCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCACTAGCTAGCCATGGACAGAAAACGCACGCGACTGCTGCATATATGCATGGCTGCATCATC
Reverse complement sequence
GATGATGCAGCCATGCATATATGCAGCAGTCGCGTGCGTTTTCTGTCCATGGCTAGCTAGTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGG[C/T]
GAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.90% | 2.60% | 0.76% | 47.65% | NA |
| All Indica | 2759 | 34.40% | 0.80% | 1.01% | 63.79% | NA |
| All Japonica | 1512 | 77.40% | 6.60% | 0.20% | 15.74% | NA |
| Aus | 269 | 19.00% | 0.00% | 1.86% | 79.18% | NA |
| Indica I | 595 | 42.50% | 0.00% | 0.17% | 57.31% | NA |
| Indica II | 465 | 27.10% | 0.20% | 1.08% | 71.61% | NA |
| Indica III | 913 | 29.10% | 1.80% | 0.99% | 68.13% | NA |
| Indica Intermediate | 786 | 38.70% | 0.60% | 1.65% | 59.03% | NA |
| Temperate Japonica | 767 | 72.40% | 2.10% | 0.39% | 25.16% | NA |
| Tropical Japonica | 504 | 83.10% | 13.30% | 0.00% | 3.57% | NA |
| Japonica Intermediate | 241 | 81.70% | 7.10% | 0.00% | 11.20% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 0.00% | 11.46% | NA |
| Intermediate | 90 | 63.30% | 3.30% | 0.00% | 33.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974479 | G -> A | LOC_Os11g10840.1 | missense_variant ; p.Ala54Thr; MODERATE | nonsynonymous_codon ; A54T | Average:38.814; most accessible tissue: Callus, score: 75.127 | possibly damaging  |
1.571 |
TOLERATED | 0.11 |
| vg1105974479 | G -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:38.814; most accessible tissue: Callus, score: 75.127 | N | N | N | N |