Search for Variation information by Variation ID:
Detailed information for vg0807401375:
| Variant ID: vg0807401375 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 7401375 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCGAAGAAGCTTGAGGGTCGACACATCATAACGGAAGTGCAAGAAGATGGACGTCCTAGTGCCCCGGCCGAAGCCGCCAAGAACTATGTACGTCACAGC[G/A]
GTTGGGTTGTGCGGGATAACGTGCCTGTCAGTACGGTGTACTGGCGAAGAACAAGGTTACGCGGAGATCATGAGAGCTTTGTCCCAGATTCGGAGAAAGA
Reverse complement sequence
TCTTTCTCCGAATCTGGGACAAAGCTCTCATGATCTCCGCGTAACCTTGTTCTTCGCCAGTACACCGTACTGACAGGCACGTTATCCCGCACAACCCAAC[C/T]
GCTGTGACGTACATAGTTCTTGGCGGCTTCGGCCGGGGCACTAGGACGTCCATCTTCTTGCACTTCCGTTATGATGTGTCGACCCTCAAGCTTCTTCGCT
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 | 39.30% | 0.20% | 1.97% | 58.55% | NA |
| All Indica | 2759 | 15.60% | 0.30% | 2.57% | 81.52% | NA |
| All Japonica | 1512 | 91.10% | 0.00% | 0.40% | 8.53% | NA |
| Aus | 269 | 1.10% | 0.00% | 3.72% | 95.17% | NA |
| Indica I | 595 | 39.70% | 0.20% | 2.35% | 57.82% | NA |
| Indica II | 465 | 12.70% | 0.90% | 4.95% | 81.51% | NA |
| Indica III | 913 | 1.90% | 0.10% | 1.75% | 96.28% | NA |
| Indica Intermediate | 786 | 15.00% | 0.40% | 2.29% | 82.32% | NA |
| Temperate Japonica | 767 | 86.70% | 0.00% | 0.39% | 12.91% | NA |
| Tropical Japonica | 504 | 96.20% | 0.00% | 0.00% | 3.77% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 1.24% | 4.56% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 5.21% | 90.62% | NA |
| Intermediate | 90 | 47.80% | 0.00% | 1.11% | 51.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0807401375 | G -> A | LOC_Os08g12500.1 | missense_variant ; p.Gly1064Ser; MODERATE | nonsynonymous_codon ; G1064S | Average:5.318; most accessible tissue: Minghui63 flag leaf, score: 9.254 | benign  |
0.709 |
DELETERIOUS | 0.00 |
| vg0807401375 | G -> DEL | LOC_Os08g12500.1 | N | frameshift_variant | Average:5.318; most accessible tissue: Minghui63 flag leaf, score: 9.254 | N | N | N | N |