Search for Variation information by Variation ID:
Detailed information for vg0609240670:
| Variant ID: vg0609240670 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9240670 |
| 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: 104. )
Flanking Sequence (100 bp) in Reference Genome:
ACAGAGCGGGGGTGCGCAGAATGAGGATTGTCCTCATCGCGCTCCACAACCAACGCTGCACTAACTACTTGGGGGGTCGCCGCTAAGTAAAGTAGCAGGG[A/G]
CTCATTTGGCTCCGGGGCGACTAGAACCGGAGGAGAGCTAAGATACGCCTTCAACTGGGCGAGGGCATTTTCAGCTTCCTCCGTCCAAGTGAACGGCCCC
Reverse complement sequence
GGGGCCGTTCACTTGGACGGAGGAAGCTGAAAATGCCCTCGCCCAGTTGAAGGCGTATCTTAGCTCTCCTCCGGTTCTAGTCGCCCCGGAGCCAAATGAG[T/C]
CCCTGCTACTTTACTTAGCGGCGACCCCCCAAGTAGTTAGTGCAGCGTTGGTTGTGGAGCGCGATGAGGACAATCCTCATTCTGCGCACCCCCGCTCTGT
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 | 12.70% | 0.10% | 4.36% | 82.84% | NA |
| All Indica | 2759 | 1.30% | 0.20% | 1.09% | 97.39% | NA |
| All Japonica | 1512 | 36.30% | 0.00% | 3.37% | 60.32% | NA |
| Aus | 269 | 0.40% | 0.00% | 42.75% | 56.88% | NA |
| Indica I | 595 | 1.20% | 0.50% | 0.84% | 97.48% | NA |
| Indica II | 465 | 0.90% | 0.20% | 0.65% | 98.28% | NA |
| Indica III | 913 | 1.60% | 0.10% | 0.77% | 97.48% | NA |
| Indica Intermediate | 786 | 1.40% | 0.00% | 1.91% | 96.69% | NA |
| Temperate Japonica | 767 | 67.90% | 0.00% | 3.39% | 28.68% | NA |
| Tropical Japonica | 504 | 1.40% | 0.00% | 0.99% | 97.62% | NA |
| Japonica Intermediate | 241 | 8.70% | 0.00% | 8.30% | 82.99% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 5.21% | 92.71% | NA |
| Intermediate | 90 | 12.20% | 0.00% | 5.56% | 82.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609240670 | A -> G | LOC_Os06g16230.1 | missense_variant ; p.Ser1124Pro; MODERATE | nonsynonymous_codon ; S1124P | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
-0.528 |
TOLERATED | 1.00 |
| vg0609240670 | A -> DEL | LOC_Os06g16230.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |