Search for Variation information by Variation ID:
Detailed information for vg0329361713:
| Variant ID: vg0329361713 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29361713 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTAACCCGTCCAACACCGTGGTGTTTGCGATGGCCAAGGCCTGCAGAAGGGGTTCTGCGCTCAGTGGAGCAACGGAAGGCGTGGGGAAGAGCCGCCTCG[A/G]
AGAGGATGCTGCGCGGCTTGGCCCGCCGATGGACGTGCCGGACTCGGGGATGTCCCCCGGACCTGGTTTGTCCTGAGCGTCGCACGAGGGAGTGGGCCCA
Reverse complement sequence
TGGGCCCACTCCCTCGTGCGACGCTCAGGACAAACCAGGTCCGGGGGACATCCCCGAGTCCGGCACGTCCATCGGCGGGCCAAGCCGCGCAGCATCCTCT[T/C]
CGAGGCGGCTCTTCCCCACGCCTTCCGTTGCTCCACTGAGCGCAGAACCCCTTCTGCAGGCCTTGGCCATCGCAAACACCACGGTGTTGGACGGGTTAAG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.00% | 0.20% | 0.47% | 43.33% | NA |
| All Indica | 2759 | 37.30% | 0.40% | 0.11% | 62.20% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.07% | 0.46% | NA |
| Aus | 269 | 0.70% | 0.00% | 0.00% | 99.26% | NA |
| Indica I | 595 | 52.90% | 0.00% | 0.00% | 47.06% | NA |
| Indica II | 465 | 37.40% | 0.20% | 0.22% | 62.15% | NA |
| Indica III | 913 | 27.70% | 0.30% | 0.11% | 71.85% | NA |
| Indica Intermediate | 786 | 36.60% | 0.80% | 0.13% | 62.47% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 52.10% | 0.00% | 18.75% | 29.17% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0329361713 | A -> DEL | LOC_Os03g51320.1 | N | frameshift_variant | Average:35.365; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | N | N | N | N |
| vg0329361713 | A -> G | LOC_Os03g51320.1 | missense_variant ; p.Ser551Pro; MODERATE | nonsynonymous_codon ; S551P | Average:35.365; most accessible tissue: Zhenshan97 flag leaf, score: 75.761 | benign  |
0.168 |
TOLERATED | 1.00 |