Search for Variation information by Variation ID:
Detailed information for vg0602082832:
| Variant ID: vg0602082832 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 2082832 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 295. )
Flanking Sequence (100 bp) in Reference Genome:
CCCCTTGTAAGTAGCACTTGTGCTCGGTCACAATGCTAACTTTCCAATAATCATTCCATTTACCCTTATATGCATGGACACGCCATGGACAATCTTCCTT[C/T]
ATGCACCTCACTTCATACACATAATTTGTTGACTTGACCACCCTAAACTCTCTCTGCAATGAAACTGCCCAATGCTTCACCGCCTCCTTCATCTCATCCT
Reverse complement sequence
AGGATGAGATGAAGGAGGCGGTGAAGCATTGGGCAGTTTCATTGCAGAGAGAGTTTAGGGTGGTCAAGTCAACAAATTATGTGTATGAAGTGAGGTGCAT[G/A]
AAGGAAGATTGTCCATGGCGTGTCCATGCATATAAGGGTAAATGGAATGATTATTGGAAAGTTAGCATTGTGACCGAGCACAAGTGCTACTTACAAGGGG
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 | 0.50% | 0.20% | 1.08% | 98.20% | NA |
| All Indica | 2759 | 0.60% | 0.10% | 0.11% | 99.13% | NA |
| All Japonica | 1512 | 0.50% | 0.40% | 0.93% | 98.21% | NA |
| Aus | 269 | 0.00% | 0.00% | 11.15% | 88.85% | NA |
| Indica I | 595 | 0.70% | 0.50% | 0.17% | 98.66% | NA |
| Indica II | 465 | 0.40% | 0.00% | 0.22% | 99.35% | NA |
| Indica III | 913 | 0.50% | 0.10% | 0.11% | 99.23% | NA |
| Indica Intermediate | 786 | 0.80% | 0.00% | 0.00% | 99.24% | NA |
| Temperate Japonica | 767 | 0.40% | 0.80% | 1.04% | 97.78% | NA |
| Tropical Japonica | 504 | 0.60% | 0.00% | 1.19% | 98.21% | NA |
| Japonica Intermediate | 241 | 0.40% | 0.00% | 0.00% | 99.59% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 4.44% | 95.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0602082832 | C -> T | LOC_Os06g04770.1 | missense_variant ; p.Met260Ile; MODERATE | nonsynonymous_codon ; M260I | Average:24.353; most accessible tissue: Minghui63 young leaf, score: 49.581 | benign  |
-0.373 |
TOLERATED | 0.56 |
| vg0602082832 | C -> DEL | LOC_Os06g04770.1 | N | frameshift_variant | Average:24.353; most accessible tissue: Minghui63 young leaf, score: 49.581 | N | N | N | N |