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Detailed information for vg1007670475:
| Variant ID: vg1007670475 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7670475 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 390. )
Flanking Sequence (100 bp) in Reference Genome:
TTCATTCATTACAATAGATAAGTACAAATGCATCAGTCACAAGGTTATGCCTTCGGTATGATCTGAACGAGCATATGCCACAGGCTCTTGGGGATCATCG[T/A]
CAAGGTCAATGTGAGGTCTTACATGAAGATTATGGTTGTATTCTTCTTCATCGACGACGTTGTCAACTCCTACAATTCGGCGCTTTCCATCCCTCACGAT
Reverse complement sequence
ATCGTGAGGGATGGAAAGCGCCGAATTGTAGGAGTTGACAACGTCGTCGATGAAGAAGAATACAACCATAATCTTCATGTAAGACCTCACATTGACCTTG[A/T]
CGATGATCCCCAAGAGCCTGTGGCATATGCTCGTTCAGATCATACCGAAGGCATAACCTTGTGACTGATGCATTTGTACTTATCTATTGTAATGAATGAA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.80% | 2.10% | 4.46% | 17.60% | NA |
| All Indica | 2759 | 75.00% | 3.10% | 6.52% | 15.40% | NA |
| All Japonica | 1512 | 73.90% | 0.30% | 1.46% | 24.34% | NA |
| Aus | 269 | 91.80% | 2.20% | 1.49% | 4.46% | NA |
| Indica I | 595 | 73.10% | 1.00% | 3.53% | 22.35% | NA |
| Indica II | 465 | 73.10% | 2.60% | 5.16% | 19.14% | NA |
| Indica III | 913 | 78.80% | 5.30% | 8.98% | 7.01% | NA |
| Indica Intermediate | 786 | 73.00% | 2.50% | 6.74% | 17.68% | NA |
| Temperate Japonica | 767 | 93.40% | 0.10% | 0.13% | 6.39% | NA |
| Tropical Japonica | 504 | 40.90% | 0.60% | 3.57% | 54.96% | NA |
| Japonica Intermediate | 241 | 80.90% | 0.40% | 1.24% | 17.43% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 1.04% | 14.58% | NA |
| Intermediate | 90 | 78.90% | 2.20% | 4.44% | 14.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007670475 | T -> A | LOC_Os10g14130.1 | missense_variant ; p.Asp479Val; MODERATE | nonsynonymous_codon ; D479V | Average:6.735; most accessible tissue: Callus, score: 17.483 | possibly damaging  |
1.838 |
TOLERATED | 0.05 |
| vg1007670475 | T -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:6.735; most accessible tissue: Callus, score: 17.483 | N | N | N | N |