Search for Variation information by Variation ID:
Detailed information for vg0719562804:
| Variant ID: vg0719562804 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19562804 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 368. )
Flanking Sequence (100 bp) in Reference Genome:
ATTCTTGGACGTACGCCACGCAATCGACGTGATGCACCTCACTAAGAACCTTTGCGTAAACCTTCTTGGCTTCCTAGGTGTATACGGAAAGTCGAAAGAT[A/G]
CACTGGAAGCACGTAATGATCTGAAGCATATGGAACAACGCGGCGACCTTCACCCGGAACCAAAGGAGAAAGGAAGCCATTACTTGAGTCCAGCCAGCTA
Reverse complement sequence
TAGCTGGCTGGACTCAAGTAATGGCTTCCTTTCTCCTTTGGTTCCGGGTGAAGGTCGCCGCGTTGTTCCATATGCTTCAGATCATTACGTGCTTCCAGTG[T/C]
ATCTTTCGACTTTCCGTATACACCTAGGAAGCCAAGAAGGTTTACGCAAAGGTTCTTAGTGAGGTGCATCACGTCGATTGCGTGGCGTACGTCCAAGAAT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.10% | 0.10% | 23.13% | 56.67% | NA |
| All Indica | 2759 | 1.20% | 0.10% | 18.09% | 80.68% | NA |
| All Japonica | 1512 | 59.70% | 0.30% | 26.59% | 13.43% | NA |
| Aus | 269 | 0.00% | 0.00% | 54.28% | 45.72% | NA |
| Indica I | 595 | 0.50% | 0.00% | 4.03% | 95.46% | NA |
| Indica II | 465 | 1.70% | 0.20% | 9.46% | 88.60% | NA |
| Indica III | 913 | 0.40% | 0.10% | 32.31% | 67.14% | NA |
| Indica Intermediate | 786 | 2.20% | 0.00% | 17.30% | 80.53% | NA |
| Temperate Japonica | 767 | 93.10% | 0.00% | 3.52% | 3.39% | NA |
| Tropical Japonica | 504 | 12.70% | 0.80% | 68.45% | 18.06% | NA |
| Japonica Intermediate | 241 | 51.90% | 0.00% | 12.45% | 35.68% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 26.04% | 73.96% | NA |
| Intermediate | 90 | 14.40% | 1.10% | 23.33% | 61.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719562804 | A -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0719562804 | A -> G | LOC_Os07g32740.1 | missense_variant ; p.Thr541Ala; MODERATE | nonsynonymous_codon ; T541A | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
1.375 |
DELETERIOUS | 0.00 |