Search for Variation information by Variation ID:
Detailed information for vg0719562918:
| Variant ID: vg0719562918 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19562918 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 322. )
Flanking Sequence (100 bp) in Reference Genome:
TAATGATCTGAAGCATATGGAACAACGCGGCGACCTTCACCCGGAACCAAAGGAGAAAGGAAGCCATTACTTGAGTCCAGCCAGCTACACTCTTAGCAAG[G/A]
CAGAGAAGGAAAGTATGTTTGAATGCTTGGAGAGCATAAAGGTACCGTCTGGATACTCCATGAATATCAAGCGAATAATAAGCACGAAGGAGAAGAAGTT
Reverse complement sequence
AACTTCTTCTCCTTCGTGCTTATTATTCGCTTGATATTCATGGAGTATCCAGACGGTACCTTTATGCTCTCCAAGCATTCAAACATACTTTCCTTCTCTG[C/T]
CTTGCTAAGAGTGTAGCTGGCTGGACTCAAGTAATGGCTTCCTTTCTCCTTTGGTTCCGGGTGAAGGTCGCCGCGTTGTTCCATATGCTTCAGATCATTA
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 | 21.30% | 5.80% | 30.49% | 42.36% | NA |
| All Indica | 2759 | 2.20% | 9.60% | 31.68% | 56.54% | NA |
| All Japonica | 1512 | 59.40% | 0.30% | 19.38% | 20.97% | NA |
| Aus | 269 | 13.40% | 0.40% | 84.76% | 1.49% | NA |
| Indica I | 595 | 1.80% | 2.70% | 21.51% | 73.95% | NA |
| Indica II | 465 | 2.20% | 9.50% | 15.70% | 72.69% | NA |
| Indica III | 913 | 1.90% | 14.90% | 44.36% | 38.88% | NA |
| Indica Intermediate | 786 | 2.80% | 8.80% | 34.10% | 54.33% | NA |
| Temperate Japonica | 767 | 93.00% | 0.00% | 3.39% | 3.65% | NA |
| Tropical Japonica | 504 | 11.70% | 0.80% | 48.81% | 38.69% | NA |
| Japonica Intermediate | 241 | 52.30% | 0.00% | 8.71% | 39.00% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 19.79% | 78.12% | NA |
| Intermediate | 90 | 14.40% | 4.40% | 30.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0719562918 | G -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:6.614; most accessible tissue: Minghui63 flower, score: 10.335 | N | N | N | N |
| vg0719562918 | G -> A | LOC_Os07g32740.1 | missense_variant ; p.Ala579Thr; MODERATE | nonsynonymous_codon ; A579T | Average:6.614; most accessible tissue: Minghui63 flower, score: 10.335 | benign  |
0.876 |
DELETERIOUS | 0.02 |