Search for Variation information by Variation ID:
Detailed information for vg0327370634:
| Variant ID: vg0327370634 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 27370634 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGACTCCGCCATGGACCCGAGGAGCTCCATCTTGAACACCGGCGAGCGCGCGGCGAGCACGGCGCGGTGTGCATGAAACGTCTCGCTGCCGACGGAGAAC[A/G]
ACACGTCCGAGCCGTCGGCACGGTCCGCGATGTCGTCGAGCTGGCCGTTGAGGTTCGACCGCGGGATGGGTATAGTGCCGTCGTCATCACCGGCATATAA
Reverse complement sequence
TTATATGCCGGTGATGACGACGGCACTATACCCATCCCGCGGTCGAACCTCAACGGCCAGCTCGACGACATCGCGGACCGTGCCGACGGCTCGGACGTGT[T/C]
GTTCTCCGTCGGCAGCGAGACGTTTCATGCACACCGCGCCGTGCTCGCCGCGCGCTCGCCGGTGTTCAAGATGGAGCTCCTCGGGTCCATGGCGGAGTCC
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 | 65.80% | 33.90% | 0.00% | 0.23% | NA |
| All Indica | 2759 | 98.40% | 1.30% | 0.00% | 0.25% | NA |
| All Japonica | 1512 | 1.30% | 98.50% | 0.00% | 0.20% | NA |
| Aus | 269 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.80% | 0.00% | 0.17% | NA |
| Indica II | 465 | 98.30% | 1.10% | 0.00% | 0.65% | NA |
| Indica III | 913 | 98.60% | 1.20% | 0.00% | 0.22% | NA |
| Indica Intermediate | 786 | 97.80% | 2.00% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 0.70% | 99.10% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 1.80% | 98.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 2.50% | 97.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 57.30% | 42.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 64.40% | 34.40% | 0.00% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0327370634 | A -> DEL | LOC_Os03g48120.1 | N | frameshift_variant | Average:79.52; most accessible tissue: Zhenshan97 panicle, score: 90.061 | N | N | N | N |
| vg0327370634 | A -> G | LOC_Os03g48120.1 | missense_variant ; p.Leu53Ser; MODERATE | nonsynonymous_codon ; L53S | Average:79.52; most accessible tissue: Zhenshan97 panicle, score: 90.061 | benign  |
-1.459 |
TOLERATED | 1.00 |