Search for Variation information by Variation ID:
Detailed information for vg0303700632:
| Variant ID: vg0303700632 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 3700632 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.02, others allele: 0.00, population size: 327. )
Flanking Sequence (100 bp) in Reference Genome:
ACAAAGGTGATCTCATCTGGCCTGACCTTCCCCTTCAGCATCTTCTCAAACATATCTATGGATTCCAGGACATGCCCATGCAGTGCCAGTCCTCCTACAA[T/C]
TGAGTTCCAAGTTGAGACGTCCTTGTCTCGCATTGACCAGAACACCTCATGTGCACTTTTCATGCTCCCACATTTTGCATACATGTCAATCAGTGCATTT
Reverse complement sequence
AAATGCACTGATTGACATGTATGCAAAATGTGGGAGCATGAAAAGTGCACATGAGGTGTTCTGGTCAATGCGAGACAAGGACGTCTCAACTTGGAACTCA[A/G]
TTGTAGGAGGACTGGCACTGCATGGGCATGTCCTGGAATCCATAGATATGTTTGAGAAGATGCTGAAGGGGAAGGTCAGGCCAGATGAGATCACCTTTGT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.60% | 1.40% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 85.10% | 14.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 7.80% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0303700632 | T -> C | LOC_Os03g07234.1 | missense_variant ; p.Ile319Val; MODERATE | nonsynonymous_codon ; I319V | Average:70.078; most accessible tissue: Zhenshan97 young leaf, score: 83.412 | benign  |
-0.137 |
TOLERATED | 0.71 |