Search for Variation information by Variation ID:
Detailed information for vg1007670968:
| Variant ID: vg1007670968 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7670968 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCATCTTGTTTGACGGTGTAAAATGTGTATCCATTTATATCGTATCCTTGCCATGTGTCTATGGTCCAAGACGGTCCCATCCCCAACAACTGTACTGTCT[C/T]
ATTTGGGACATCCATGGACATTGTCACACGATTCTTGAACCATTCGTTGAACCGAGAATTATGTTCTCTGTTAATCCATGCATCAGATCGCCCCAAGTTC
Reverse complement sequence
GAACTTGGGGCGATCTGATGCATGGATTAACAGAGAACATAATTCTCGGTTCAACGAATGGTTCAAGAATCGTGTGACAATGTCCATGGATGTCCCAAAT[G/A]
AGACAGTACAGTTGTTGGGGATGGGACCGTCTTGGACCATAGACACATGGCAAGGATACGATATAAATGGATACACATTTTACACCGTCAAACAAGATGA
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 | 33.00% | 8.10% | 15.68% | 43.29% | NA |
| All Indica | 2759 | 11.60% | 13.70% | 17.40% | 57.38% | NA |
| All Japonica | 1512 | 57.80% | 0.00% | 14.95% | 27.25% | NA |
| Aus | 269 | 98.10% | 0.00% | 1.49% | 0.37% | NA |
| Indica I | 595 | 5.40% | 11.60% | 9.41% | 73.61% | NA |
| Indica II | 465 | 6.70% | 25.60% | 21.94% | 45.81% | NA |
| Indica III | 913 | 14.50% | 10.40% | 18.29% | 56.85% | NA |
| Indica Intermediate | 786 | 15.80% | 12.00% | 19.72% | 52.54% | NA |
| Temperate Japonica | 767 | 69.40% | 0.00% | 23.86% | 6.78% | NA |
| Tropical Japonica | 504 | 32.10% | 0.00% | 6.35% | 61.51% | NA |
| Japonica Intermediate | 241 | 74.70% | 0.00% | 4.56% | 20.75% | NA |
| VI/Aromatic | 96 | 67.70% | 0.00% | 14.58% | 17.71% | NA |
| Intermediate | 90 | 40.00% | 4.40% | 18.89% | 36.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007670968 | C -> T | LOC_Os10g14130.1 | missense_variant ; p.Glu315Lys; MODERATE | nonsynonymous_codon ; E315K | Average:12.724; most accessible tissue: Zhenshan97 panicle, score: 20.424 | benign  |
1.285 |
TOLERATED | 0.16 |
| vg1007670968 | C -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:12.724; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |