Search for Variation information by Variation ID:
Detailed information for vg0202539942:
| Variant ID: vg0202539942 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2539942 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 227. )
Flanking Sequence (100 bp) in Reference Genome:
GACATCAAACGTCGACAATGGCGCGCTAGGTAGGGGGAGTTTGGTACTTCAAGGTTTCGACGAGATGGGTTCAAAAGATGGATTCTCTGACAACAAGCTA[T/C]
TCGACGACTTCGCTGTGGGAAGATCCAACCCGACCGAAGTATGTCTCCCGACGAGATCGGAACCATCGTCATCAACAACTCGATCTCTCGAGATCGACCA
Reverse complement sequence
TGGTCGATCTCGAGAGATCGAGTTGTTGATGACGATGGTTCCGATCTCGTCGGGAGACATACTTCGGTCGGGTTGGATCTTCCCACAGCGAAGTCGTCGA[A/G]
TAGCTTGTTGTCAGAGAATCCATCTTTTGAACCCATCTCGTCGAAACCTTGAAGTACCAAACTCCCCCTACCTAGCGCGCCATTGTCGACGTTTGATGTC
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 | 95.80% | 4.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 96.90% | 3.10% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.70% | 5.20% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 6.20% | 93.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 11.10% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0202539942 | T -> C | LOC_Os02g05290.1 | missense_variant ; p.Phe13Leu; MODERATE | nonsynonymous_codon ; F13L | Average:45.863; most accessible tissue: Minghui63 young leaf, score: 61.887 | benign  |
-0.499 |
TOLERATED | 1.00 |