302 variations found. LOC_Os02g40190 (receptor kinase; putative; expressed), ranging from 24,323,431 bp to 24,324,493 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0224323440 (J) | chr02 | 24323440 | G | T | 61.80% | 36.63% | G -> T | NA |
LOC_Os02g40190.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.043; most accessible tissue: Callus, score: 90.934 |
| vg0224323443 (J) | chr02 | 24323443 | C | T | 62.90% | 35.51% | C -> T | NA |
LOC_Os02g40190.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.043; most accessible tissue: Callus, score: 90.934 |
| vg0224323446 (J) | chr02 | 24323446 | C | T | 61.30% | 35.78% | C -> T | NA |
LOC_Os02g40190.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.043; most accessible tissue: Callus, score: 90.934 |
| vg0224323451 (J) | chr02 | 24323451 | G | A | 61.30% | 35.72% | G -> A | NA |
LOC_Os02g40190.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.043; most accessible tissue: Callus, score: 90.934 |
| vg0224323456 (J) | chr02 | 24323456 | ACT | A | 62.00% | 36.01% | ACT -> A | NA |
LOC_Os02g40190.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.043; most accessible tissue: Callus, score: 90.934 |
| vg0224323458 (J) | chr02 | 24323458 | T | A | 55.40% | 36.65% | T -> A |
LOC_Os02g40190.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.043; most accessible tissue: Callus, score: 90.934 |
|
| vg0224323467 (J) | chr02 | 24323467 | A | G | 62.30% | 35.29% | A -> G | NA |
LOC_Os02g40190.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.043; most accessible tissue: Callus, score: 90.934 |
| vg0224323470 (J) | chr02 | 24323470 | G | T | 60.90% | 36.73% | G -> T | NA |
LOC_Os02g40190.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.043; most accessible tissue: Callus, score: 90.934 |
| vg0224323473 (J) | chr02 | 24323473 | T | G | 59.60% | 37.66% | T -> G | NA |
LOC_Os02g40190.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.708; most accessible tissue: Callus, score: 90.934 |
| vg0224323474 (J) | chr02 | 24323474 | T | TG | 61.80% | 35.32% | T -> TG | NA |
LOC_Os02g40190.1 Alt: TG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.708; most accessible tissue: Callus, score: 90.934 |
| vg0224323479 (J) | chr02 | 24323479 | A | G | 60.50% | 34.26% | A -> G |
LOC_Os02g40190.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.708; most accessible tissue: Callus, score: 90.934 |
|
| vg0224323482 (J) | chr02 | 24323482 | A | G | 34.30% | 37.83% | G -> A |
LOC_Os02g40190.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.042; most accessible tissue: Callus, score: 90.934 |
|
| vg0224323483 (J) | chr02 | 24323483 | C | T | 63.00% | 35.23% | C -> T | NA |
LOC_Os02g40190.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 26.130; most accessible tissue: Callus, score: 90.934 |
| vg0224323484 (J) | chr02 | 24323484 | CA | C | 62.90% | 35.27% | CA -> C,TA,GA | NA |
LOC_Os02g40190.1 Alt: TA| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g40190.1 Alt: GA| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os02g40190.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 26.130; most accessible tissue: Callus, score: 90.934 |
| vg0224323492 (J) | chr02 | 24323492 | A | C | 62.50% | 36.25% | A -> C | NA |
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g40190.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 27.546; most accessible tissue: Callus, score: 90.934 |
| vg0224323495 (J) | chr02 | 24323495 | G | T | 62.10% | 35.12% | G -> T | NA |
LOC_Os02g40190.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 28.036; most accessible tissue: Callus, score: 90.934 |
| vg0224323516 (J) | chr02 | 24323516 | G | C | 42.40% | 40.69% | C -> G | NA |
LOC_Os02g40190.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 28.713; most accessible tissue: Callus, score: 90.934 |
| vg0224323522 (J) | chr02 | 24323522 | A | G | 42.40% | 40.82% | G -> A | NA |
LOC_Os02g40190.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 29.038; most accessible tissue: Callus, score: 90.934 |
| vg0224323530 (J) | chr02 | 24323530 | C | CA | 62.10% | 35.78% | C -> CA | NA |
LOC_Os02g40190.1 Alt: CA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 29.206; most accessible tissue: Callus, score: 90.934 |
| vg0224323551 (J) | chr02 | 24323551 | A | G | 59.60% | 35.95% | A -> G | NA |
LOC_Os02g40190.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 32.567; most accessible tissue: Callus, score: 90.934 |
| vg0224323558 (J) | chr02 | 24323558 | A | T | 62.20% | 35.89% | A -> T | NA |
LOC_Os02g40190.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 33.078; most accessible tissue: Callus, score: 90.934 |
| vg0224323567 (J) | chr02 | 24323567 | C | T | 63.80% | 34.79% | C -> T | NA |
LOC_Os02g40190.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 35.881; most accessible tissue: Callus, score: 90.934 |
| vg0224323572 (J) | chr02 | 24323572 | C | T | 60.00% | 36.06% | C -> T | NA |
LOC_Os02g40190.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 36.391; most accessible tissue: Callus, score: 90.934 |
| vg0224323574 (J) | chr02 | 24323574 | A | Unkown | 62.70% | 36.12% | A -> C | NA |
LOC_Os02g40190.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os02g40200.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g40180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 36.391; most accessible tissue: Callus, score: 90.934 |
| vg0224323578 (J) | chr02 | 24323578 | G | C | 30.50% | 39.44% | G -> A,C | NA |
LOC_Os02g40190.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os02g40190.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g40190.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 34.422; most accessible tissue: Callus, score: 69.280 |
Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China
Comments or Questions? Please contact us. Our website: http://xielab.ncpgr.cn/