Search for Variation information by Variation ID:
Detailed information for vg1007738770:
| Variant ID: vg1007738770 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7738770 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGTTGGAGGTGGTGGTCTATAAGCAGCAGCGAGCTGCGCCATGTCGATGGTCTGCCACTGAACTGCTCCTTGCGGTGCCTGTGGGGCTGCCCCTGCGACG[G/C]
CGGAGTGGTTTCCGACAACTGTGTGCCCACTGAATACCGCGTGGTGAAGGTCAATGTGCTTCAGAGGATCATTCCTGAAGCTTAAGACACCTTTATTTTG
Reverse complement sequence
CAAAATAAAGGTGTCTTAAGCTTCAGGAATGATCCTCTGAAGCACATTGACCTTCACCACGCGGTATTCAGTGGGCACACAGTTGTCGGAAACCACTCCG[C/G]
CGTCGCAGGGGCAGCCCCACAGGCACCGCAAGGAGCAGTTCAGTGGCAGACCATCGACATGGCGCAGCTCGCTGCTGCTTATAGACCACCACCTCCAACT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 71.20% | 0.20% | 10.56% | 18.03% | NA |
| All Indica | 2759 | 69.20% | 0.10% | 11.82% | 18.85% | NA |
| All Japonica | 1512 | 74.00% | 0.00% | 5.09% | 20.90% | NA |
| Aus | 269 | 67.30% | 1.50% | 30.86% | 0.37% | NA |
| Indica I | 595 | 61.80% | 0.00% | 16.47% | 21.68% | NA |
| Indica II | 465 | 68.40% | 0.00% | 11.18% | 20.43% | NA |
| Indica III | 913 | 75.70% | 0.30% | 8.87% | 15.12% | NA |
| Indica Intermediate | 786 | 67.70% | 0.10% | 12.09% | 20.10% | NA |
| Temperate Japonica | 767 | 80.40% | 0.00% | 1.43% | 18.12% | NA |
| Tropical Japonica | 504 | 65.70% | 0.00% | 11.71% | 22.62% | NA |
| Japonica Intermediate | 241 | 71.00% | 0.00% | 2.90% | 26.14% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 4.17% | 6.25% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 10.00% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007738770 | G -> C | LOC_Os10g14290.1 | missense_variant ; p.Ala247Gly; MODERATE | nonsynonymous_codon ; A247G | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
1.283 |
TOLERATED | 0.08 |
| vg1007738770 | G -> DEL | LOC_Os10g14290.1 | N | frameshift_variant | Average:4.415; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |