Search for Variation information by Variation ID:
Detailed information for vg0702311601:
| Variant ID: vg0702311601 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 2311601 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 277. )
Flanking Sequence (100 bp) in Reference Genome:
GCACTTCAACGTGCCGTCGGCGGCGGCGAGCCTGTCACAGCTCGTCTCCAACATGATCGAGGACGACTGCACGACGAACGGGGTGCCTCTCCCCAACGTC[G/T]
CCTCCAAGGTCCTCGCCAAGGTCATCGAATACTGCATCAAGCACGCCGCCGCCGGGGAGGAGGAGGAGAAGGATCTGAAGAGCTTCGACGCCGAGTTCAT
Reverse complement sequence
ATGAACTCGGCGTCGAAGCTCTTCAGATCCTTCTCCTCCTCCTCCCCGGCGGCGGCGTGCTTGATGCAGTATTCGATGACCTTGGCGAGGACCTTGGAGG[C/A]
GACGTTGGGGAGAGGCACCCCGTTCGTCGTGCAGTCGTCCTCGATCATGTTGGAGACGAGCTGTGACAGGCTCGCCGCCGCCGACGGCACGTTGAAGTGC
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 | 99.30% | 0.60% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 98.10% | 1.80% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.00% | 4.80% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0702311601 | G -> T | LOC_Os07g05180.1 | missense_variant ; p.Ala62Ser; MODERATE | nonsynonymous_codon ; A62S | Average:60.41; most accessible tissue: Zhenshan97 panicle, score: 82.888 | benign  |
0.343 |
TOLERATED | 0.28 |