Search for Variation information by Variation ID:
Detailed information for vg1007670593:
| Variant ID: vg1007670593 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7670593 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 345. )
Flanking Sequence (100 bp) in Reference Genome:
CTTACATGAAGATTATGGTTGTATTCTTCTTCATCGACGACGTTGTCAACTCCTACAATTCGGCGCTTTCCATCCCTCACGATGTGCATCTTCTTGTTTG[A/C]
AGGGTCTTTTATGTAGAATATCTGCTCGACCTGTTTCGCAAGTACAAATGGTTCATCGGCGTATCCCACCTTATATAGATCTACTAAAGTGAAACCTTCC
Reverse complement sequence
GGAAGGTTTCACTTTAGTAGATCTATATAAGGTGGGATACGCCGATGAACCATTTGTACTTGCGAAACAGGTCGAGCAGATATTCTACATAAAAGACCCT[T/G]
CAAACAAGAAGATGCACATCGTGAGGGATGGAAAGCGCCGAATTGTAGGAGTTGACAACGTCGTCGATGAAGAAGAATACAACCATAATCTTCATGTAAG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 25.10% | 0.50% | 20.50% | 53.94% | NA |
| All Indica | 2759 | 6.60% | 0.60% | 18.63% | 74.19% | NA |
| All Japonica | 1512 | 47.50% | 0.40% | 23.35% | 28.77% | NA |
| Aus | 269 | 79.60% | 0.00% | 19.70% | 0.74% | NA |
| Indica I | 595 | 4.20% | 0.50% | 11.93% | 83.36% | NA |
| Indica II | 465 | 6.50% | 0.40% | 24.52% | 68.60% | NA |
| Indica III | 913 | 5.80% | 0.00% | 19.82% | 74.37% | NA |
| Indica Intermediate | 786 | 9.40% | 1.40% | 18.83% | 70.36% | NA |
| Temperate Japonica | 767 | 55.70% | 0.80% | 34.68% | 8.87% | NA |
| Tropical Japonica | 504 | 26.60% | 0.00% | 12.70% | 60.71% | NA |
| Japonica Intermediate | 241 | 65.10% | 0.00% | 9.54% | 25.31% | NA |
| VI/Aromatic | 96 | 37.50% | 0.00% | 32.29% | 30.21% | NA |
| Intermediate | 90 | 38.90% | 1.10% | 20.00% | 40.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007670593 | A -> C | LOC_Os10g14130.1 | missense_variant ; p.Ser440Ala; MODERATE | nonsynonymous_codon ; S440A | Average:6.584; most accessible tissue: Callus, score: 15.821 | benign  |
-0.187 |
TOLERATED | 0.56 |
| vg1007670593 | A -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:6.584; most accessible tissue: Callus, score: 15.821 | N | N | N | N |