Search for Variation information by Variation ID:
Detailed information for vg1007670982:
| Variant ID: vg1007670982 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7670982 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGTGTAAAATGTGTATCCATTTATATCGTATCCTTGCCATGTGTCTATGGTCCAAGACGGTCCCATCCCCAACAACTGTACTGTCTCATTTGGGACATCC[A/G]
TGGACATTGTCACACGATTCTTGAACCATTCGTTGAACCGAGAATTATGTTCTCTGTTAATCCATGCATCAGATCGCCCCAAGTTCTCATCTCAGATTTT
Reverse complement sequence
AAAATCTGAGATGAGAACTTGGGGCGATCTGATGCATGGATTAACAGAGAACATAATTCTCGGTTCAACGAATGGTTCAAGAATCGTGTGACAATGTCCA[T/C]
GGATGTCCCAAATGAGACAGTACAGTTGTTGGGGATGGGACCGTCTTGGACCATAGACACATGGCAAGGATACGATATAAATGGATACACATTTTACACC
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 | 46.00% | 0.30% | 14.94% | 38.85% | NA |
| All Indica | 2759 | 34.40% | 0.40% | 16.09% | 49.04% | NA |
| All Japonica | 1512 | 56.80% | 0.00% | 14.48% | 28.70% | NA |
| Aus | 269 | 92.90% | 0.00% | 6.32% | 0.74% | NA |
| Indica I | 595 | 19.50% | 0.30% | 9.41% | 70.76% | NA |
| Indica II | 465 | 38.30% | 0.60% | 23.44% | 37.63% | NA |
| Indica III | 913 | 38.20% | 0.40% | 18.51% | 42.83% | NA |
| Indica Intermediate | 786 | 39.10% | 0.40% | 13.99% | 46.56% | NA |
| Temperate Japonica | 767 | 67.10% | 0.00% | 25.16% | 7.69% | NA |
| Tropical Japonica | 504 | 33.50% | 0.00% | 2.78% | 63.69% | NA |
| Japonica Intermediate | 241 | 72.60% | 0.00% | 4.98% | 22.41% | NA |
| VI/Aromatic | 96 | 66.70% | 0.00% | 13.54% | 19.79% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 14.44% | 31.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007670982 | A -> G | LOC_Os10g14130.1 | missense_variant ; p.Met310Thr; MODERATE | nonsynonymous_codon ; M310T | Average:12.724; most accessible tissue: Zhenshan97 panicle, score: 20.424 | benign  |
-0.525 |
TOLERATED | 1.00 |
| vg1007670982 | A -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:12.724; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |