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Detailed information for vg0710349951:
| Variant ID: vg0710349951 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10349951 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGTAAGATTTAGCCATTCCGCTAGTTGCTGCTTATATATGTTGATTACTAATAAATAATCTCTCACAACATGAAGGTGGCGTCGGGCATGGCCATCCCAA[C/T]
GGACCCTTCAGGTACTTACCACTGCAGGCCGATTCCAGCAGGATACTCGAAGGTCGAAGTTGAGTTGGTCGAAGGCGCGTACGAGGACCTCGAGCTGGAT
Reverse complement sequence
ATCCAGCTCGAGGTCCTCGTACGCGCCTTCGACCAACTCAACTTCGACCTTCGAGTATCCTGCTGGAATCGGCCTGCAGTGGTAAGTACCTGAAGGGTCC[G/A]
TTGGGATGGCCATGCCCGACGCCACCTTCATGTTGTGAGAGATTATTTATTAGTAATCAACATATATAAGCAGCAACTAGCGGAATGGCTAAATCTTACC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.70% | 0.60% | 6.14% | 63.56% | NA |
| All Indica | 2759 | 5.40% | 0.10% | 3.19% | 91.34% | NA |
| All Japonica | 1512 | 71.30% | 1.70% | 12.30% | 14.68% | NA |
| Aus | 269 | 50.90% | 0.00% | 4.46% | 44.61% | NA |
| Indica I | 595 | 7.10% | 0.00% | 2.02% | 90.92% | NA |
| Indica II | 465 | 6.70% | 0.00% | 2.15% | 91.18% | NA |
| Indica III | 913 | 2.70% | 0.10% | 0.55% | 96.60% | NA |
| Indica Intermediate | 786 | 6.50% | 0.10% | 7.76% | 85.62% | NA |
| Temperate Japonica | 767 | 57.60% | 0.10% | 17.47% | 24.77% | NA |
| Tropical Japonica | 504 | 87.70% | 5.00% | 3.37% | 3.97% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 14.52% | 4.98% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 1.04% | 95.83% | NA |
| Intermediate | 90 | 40.00% | 1.10% | 3.33% | 55.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0710349951 | C -> DEL | LOC_Os07g17510.1 | N | frameshift_variant | Average:4.776; most accessible tissue: Callus, score: 7.869 | N | N | N | N |
| vg0710349951 | C -> T | LOC_Os07g17510.1 | missense_variant ; p.Thr483Met; MODERATE | nonsynonymous_codon ; T483M | Average:4.776; most accessible tissue: Callus, score: 7.869 | benign  |
1.315 |
DELETERIOUS | 0.05 |