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Detailed information for vg1007670457:
| Variant ID: vg1007670457 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7670457 |
| 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: 390. )
Flanking Sequence (100 bp) in Reference Genome:
TGCAATAAAACAAAATACTTCATTCATTACAATAGATAAGTACAAATGCATCAGTCACAAGGTTATGCCTTCGGTATGATCTGAACGAGCATATGCCACA[G/A]
GCTCTTGGGGATCATCGTCAAGGTCAATGTGAGGTCTTACATGAAGATTATGGTTGTATTCTTCTTCATCGACGACGTTGTCAACTCCTACAATTCGGCG
Reverse complement sequence
CGCCGAATTGTAGGAGTTGACAACGTCGTCGATGAAGAAGAATACAACCATAATCTTCATGTAAGACCTCACATTGACCTTGACGATGATCCCCAAGAGC[C/T]
TGTGGCATATGCTCGTTCAGATCATACCGAAGGCATAACCTTGTGACTGATGCATTTGTACTTATCTATTGTAATGAATGAAGTATTTTGTTTTATTGCA
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 | 81.50% | 0.10% | 1.02% | 17.41% | NA |
| All Indica | 2759 | 83.50% | 0.20% | 0.94% | 15.40% | NA |
| All Japonica | 1512 | 75.00% | 0.00% | 1.19% | 23.81% | NA |
| Aus | 269 | 95.50% | 0.00% | 0.00% | 4.46% | NA |
| Indica I | 595 | 76.10% | 0.00% | 1.51% | 22.35% | NA |
| Indica II | 465 | 79.40% | 0.00% | 1.51% | 19.14% | NA |
| Indica III | 913 | 92.40% | 0.40% | 0.11% | 7.01% | NA |
| Indica Intermediate | 786 | 81.00% | 0.10% | 1.15% | 17.68% | NA |
| Temperate Japonica | 767 | 93.50% | 0.00% | 0.13% | 6.39% | NA |
| Tropical Japonica | 504 | 43.30% | 0.00% | 3.37% | 53.37% | NA |
| Japonica Intermediate | 241 | 82.60% | 0.00% | 0.00% | 17.43% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 2.08% | 13.54% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1007670457 | G -> A | LOC_Os10g14130.1 | missense_variant ; p.Pro485Leu; MODERATE | nonsynonymous_codon ; P485L | Average:6.735; most accessible tissue: Callus, score: 17.483 | benign  |
0.262 |
TOLERATED | 0.06 |
| vg1007670457 | G -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:6.735; most accessible tissue: Callus, score: 17.483 | N | N | N | N |