Search for Variation information by Variation ID:
Detailed information for vg0719562979:
| Variant ID: vg0719562979 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19562979 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 395. )
Flanking Sequence (100 bp) in Reference Genome:
AGCCATTACTTGAGTCCAGCCAGCTACACTCTTAGCAAGGCAGAGAAGGAAAGTATGTTTGAATGCTTGGAGAGCATAAAGGTACCGTCTGGATACTCCA[T/C]
GAATATCAAGCGAATAATAAGCACGAAGGAGAAGAAGTTCACAAACCTAAAGTCTCATGACTGTCACGTGTTGATGACACAACTGCTACCAGTTGTAATA
Reverse complement sequence
TATTACAACTGGTAGCAGTTGTGTCATCAACACGTGACAGTCATGAGACTTTAGGTTTGTGAACTTCTTCTCCTTCGTGCTTATTATTCGCTTGATATTC[A/G]
TGGAGTATCCAGACGGTACCTTTATGCTCTCCAAGCATTCAAACATACTTTCCTTCTCTGCCTTGCTAAGAGTGTAGCTGGCTGGACTCAAGTAATGGCT
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 | 13.10% | 7.00% | 23.00% | 56.92% | NA |
| All Indica | 2759 | 1.30% | 0.10% | 20.48% | 78.11% | NA |
| All Japonica | 1512 | 37.80% | 21.40% | 21.36% | 19.38% | NA |
| Aus | 269 | 0.00% | 0.00% | 65.80% | 34.20% | NA |
| Indica I | 595 | 0.80% | 0.00% | 3.36% | 95.80% | NA |
| Indica II | 465 | 2.20% | 0.00% | 17.20% | 80.65% | NA |
| Indica III | 913 | 0.70% | 0.00% | 36.04% | 63.31% | NA |
| Indica Intermediate | 786 | 2.00% | 0.30% | 17.30% | 80.41% | NA |
| Temperate Japonica | 767 | 55.00% | 37.90% | 2.61% | 4.43% | NA |
| Tropical Japonica | 504 | 10.30% | 0.80% | 54.37% | 34.52% | NA |
| Japonica Intermediate | 241 | 40.70% | 12.00% | 12.03% | 35.27% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 2.08% | 97.92% | NA |
| Intermediate | 90 | 12.20% | 3.30% | 22.22% | 62.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719562979 | T -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:7.428; most accessible tissue: Zhenshan97 flag leaf, score: 11.736 | N | N | N | N |
| vg0719562979 | T -> C | LOC_Os07g32740.1 | missense_variant ; p.Met599Thr; MODERATE | nonsynonymous_codon ; M599T | Average:7.428; most accessible tissue: Zhenshan97 flag leaf, score: 11.736 | benign  |
-0.948 |
TOLERATED | 1.00 |