Search for Variation information by Variation ID:
Detailed information for vg0719562789:
| Variant ID: vg0719562789 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19562789 |
| 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: 381. )
Flanking Sequence (100 bp) in Reference Genome:
GTTACCATATTGGGAATTCTTGGACGTACGCCACGCAATCGACGTGATGCACCTCACTAAGAACCTTTGCGTAAACCTTCTTGGCTTCCTAGGTGTATAC[G/A]
GAAAGTCGAAAGATACACTGGAAGCACGTAATGATCTGAAGCATATGGAACAACGCGGCGACCTTCACCCGGAACCAAAGGAGAAAGGAAGCCATTACTT
Reverse complement sequence
AAGTAATGGCTTCCTTTCTCCTTTGGTTCCGGGTGAAGGTCGCCGCGTTGTTCCATATGCTTCAGATCATTACGTGCTTCCAGTGTATCTTTCGACTTTC[C/T]
GTATACACCTAGGAAGCCAAGAAGGTTTACGCAAAGGTTCTTAGTGAGGTGCATCACGTCGATTGCGTGGCGTACGTCCAAGAATTCCCAATATGGTAAC
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 | 21.90% | 0.20% | 20.61% | 57.24% | NA |
| All Indica | 2759 | 1.60% | 0.10% | 16.96% | 81.37% | NA |
| All Japonica | 1512 | 64.50% | 0.50% | 21.63% | 13.43% | NA |
| Aus | 269 | 0.00% | 0.00% | 50.93% | 49.07% | NA |
| Indica I | 595 | 0.50% | 0.00% | 4.54% | 94.96% | NA |
| Indica II | 465 | 2.60% | 0.40% | 6.88% | 90.11% | NA |
| Indica III | 913 | 0.90% | 0.10% | 31.54% | 67.47% | NA |
| Indica Intermediate | 786 | 2.50% | 0.00% | 15.39% | 82.06% | NA |
| Temperate Japonica | 767 | 93.50% | 0.00% | 3.39% | 3.13% | NA |
| Tropical Japonica | 504 | 24.00% | 1.40% | 52.18% | 22.42% | NA |
| Japonica Intermediate | 241 | 56.80% | 0.00% | 15.77% | 27.39% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 23.96% | 76.04% | NA |
| Intermediate | 90 | 20.00% | 1.10% | 21.11% | 57.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719562789 | G -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:4.73; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg0719562789 | G -> A | LOC_Os07g32740.1 | missense_variant ; p.Gly536Arg; MODERATE | nonsynonymous_codon ; G536R | Average:4.73; most accessible tissue: Zhenshan97 root, score: 10.511 | benign  |
1.042 |
DELETERIOUS | 0.02 |