12 variations found. LOC_Os11g44460 (expressed protein), ranging from 26,903,329 bp to 26,903,674 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Color | Explain | Details |
|---|---|---|
| red | High impact variants defined by snpEff | 'STOP_LOST', 'START_LOST', 'STOP_GAINED', 'FRAME_SHIFT' et. al., the details can be found at http://snpef f.sourceforge.net/SnpEff_manual.html#eff. |
| purple | 'Damaging' or 'probably damaging' non-synonymous SNPs defined by PolyPhen-2 | This is a qualitative result of nonsynonymous SNP annotation, where 'damaging' or 'probably damaging' means that the variant is more likely to affect protein function. Details can be found here. |
| Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
|---|---|---|---|---|---|---|---|---|---|
| vg1126903366 (J) | chr11 | 26903366 | G | A | 68.80% | 29.12% | G -> A | NA |
LOC_Os11g44460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g44460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.198; most accessible tissue: Callus, score: 46.436 |
| vg1126903372 (J) | chr11 | 26903372 | A | G | 48.40% | 31.06% | G -> A | NA |
LOC_Os11g44460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g44460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.254; most accessible tissue: Callus, score: 46.436 |
| vg1126903377 (J) | chr11 | 26903377 | AGAG | A | 68.30% | 29.12% | AGAG -> A | NA |
LOC_Os11g44460.1 Alt: A| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os11g44460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.198; most accessible tissue: Callus, score: 46.436 |
| vg1126903384 (J) | chr11 | 26903384 | G | A | 69.70% | 29.16% | G -> A | NA |
LOC_Os11g44460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g44460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.591; most accessible tissue: Callus, score: 46.436 |
| vg1126903414 (J) | chr11 | 26903414 | T | C | 46.80% | 31.17% | C -> T | NA |
LOC_Os11g44460.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g44460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 14.561; most accessible tissue: Callus, score: 46.436 |
| vg1126903423 (J) | chr11 | 26903423 | G | T | 46.70% | 31.17% | T -> G | NA |
LOC_Os11g44460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g44460.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 14.505; most accessible tissue: Callus, score: 46.436 |
| vg1126903435 (J) | chr11 | 26903435 | T | C | 42.10% | 33.71% | C -> T | NA |
LOC_Os11g44460.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g44460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.004; most accessible tissue: Callus, score: 62.316 |
| vg1126903438 (J) | chr11 | 26903438 | G | T | 21.40% | 75.75% | G -> T | NA |
LOC_Os11g44460.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g44460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.004; most accessible tissue: Callus, score: 62.316 |
| vg1126903440 (J) | chr11 | 26903440 | C | T | 20.70% | 74.95% | C -> T | NA |
LOC_Os11g44460.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g44460.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.645; most accessible tissue: Callus, score: 62.316 |
| vg1126903458 (J) | chr11 | 26903458 | T | C | 17.60% | 81.85% | T -> C | NA |
LOC_Os11g44460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g44460.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 15.068; most accessible tissue: Callus, score: 62.316 |
| vg1126903465 (J) | chr11 | 26903465 | A | C | 17.40% | 82.04% | A -> C | NA |
LOC_Os11g44460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g44460.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 15.179; most accessible tissue: Callus, score: 62.316 |
| vg1126903582 (J) | chr11 | 26903582 | T | C | 17.20% | 81.55% | T -> C | NA |
LOC_Os11g44460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g44460.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 12.252; most accessible tissue: Callus, score: 33.952 |