Search for Variation information by Variation ID:
Detailed information for vg1007670937:
| Variant ID: vg1007670937 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7670937 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 404. )
Flanking Sequence (100 bp) in Reference Genome:
ACGGACGTCGCTGTTTTGCACTGTGCTTTTGTCATCTTGTTTGACGGTGTAAAATGTGTATCCATTTATATCGTATCCTTGCCATGTGTCTATGGTCCAA[G/C]
ACGGTCCCATCCCCAACAACTGTACTGTCTCATTTGGGACATCCATGGACATTGTCACACGATTCTTGAACCATTCGTTGAACCGAGAATTATGTTCTCT
Reverse complement sequence
AGAGAACATAATTCTCGGTTCAACGAATGGTTCAAGAATCGTGTGACAATGTCCATGGATGTCCCAAATGAGACAGTACAGTTGTTGGGGATGGGACCGT[C/G]
TTGGACCATAGACACATGGCAAGGATACGATATAAATGGATACACATTTTACACCGTCAAACAAGATGACAAAAGCACAGTGCAAAACAGCGACGTCCGT
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 | 55.40% | 6.20% | 21.16% | 17.22% | NA |
| All Indica | 2759 | 57.70% | 0.10% | 24.94% | 17.18% | NA |
| All Japonica | 1512 | 44.30% | 18.40% | 16.67% | 20.63% | NA |
| Aus | 269 | 96.70% | 0.00% | 3.35% | 0.00% | NA |
| Indica I | 595 | 35.60% | 0.20% | 45.04% | 19.16% | NA |
| Indica II | 465 | 75.10% | 0.00% | 16.13% | 8.82% | NA |
| Indica III | 913 | 57.70% | 0.20% | 19.28% | 22.78% | NA |
| Indica Intermediate | 786 | 64.20% | 0.10% | 21.50% | 14.12% | NA |
| Temperate Japonica | 767 | 45.40% | 32.70% | 16.04% | 5.87% | NA |
| Tropical Japonica | 504 | 34.50% | 1.20% | 18.25% | 46.03% | NA |
| Japonica Intermediate | 241 | 61.40% | 8.70% | 15.35% | 14.52% | NA |
| VI/Aromatic | 96 | 44.80% | 5.20% | 32.29% | 17.71% | NA |
| Intermediate | 90 | 58.90% | 6.70% | 22.22% | 12.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007670937 | G -> C | LOC_Os10g14130.1 | missense_variant ; p.Ser325Cys; MODERATE | nonsynonymous_codon ; S325C | Average:12.339; most accessible tissue: Callus, score: 18.912 | benign  |
0.133 |
TOLERATED | 0.06 |
| vg1007670937 | G -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:12.339; most accessible tissue: Callus, score: 18.912 | N | N | N | N |