50 variations found. LOC_Os04g32560 (ATP-dependent Clp protease ATP-binding subunit clpA homolog CD4B;chloroplast precursor; putative; expressed), ranging from 19,601,286 bp to 19,607,918 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0419601306 (J) | chr04 | 19601306 | AC | A | 98.60% | 0.00% | AC -> A | NA |
LOC_Os04g32560.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32560.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32550.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.164; most accessible tissue: Callus, score: 92.669 |
| vg0419601360 (J) | chr04 | 19601360 | A | G | 96.90% | 0.00% | A -> G | NA |
LOC_Os04g32560.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32560.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.526; most accessible tissue: Minghui63 flag leaf, score: 88.342 |
| vg0419601384 (J) | chr04 | 19601384 | A | T | 58.30% | 0.36% | T -> A |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g32560.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32550.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.893; most accessible tissue: Minghui63 flag leaf, score: 89.718 |
|
| vg0419601448 (J) | chr04 | 19601448 | A | G | 98.00% | 0.00% | A -> G | NA |
LOC_Os04g32560.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32560.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.394; most accessible tissue: Callus, score: 89.397 |
| vg0419601464 (J) | chr04 | 19601464 | G | A | 98.60% | 0.00% | G -> A | NA |
LOC_Os04g32560.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32560.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32550.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.262; most accessible tissue: Callus, score: 89.397 |
| vg0419601548 (J) | chr04 | 19601548 | G | T | 58.70% | 0.00% | T -> G |
LOC_Os04g32560.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32560.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.808; most accessible tissue: Callus, score: 89.397 |
|
| vg0419602687 (J) | chr04 | 19602687 | C | T | 58.50% | 0.38% | T -> C |
LOC_Os04g32560.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g32560.2 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os04g32560.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os04g32560.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 86.701; most accessible tissue: Minghui63 flag leaf, score: 94.147 |
|
| vg0419602807 (J) | chr04 | 19602807 | A | G | 97.30% | 0.00% | A -> G |
LOC_Os04g32560.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g32560.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 81.325; most accessible tissue: Minghui63 flag leaf, score: 91.351 |
|
| vg0419602852 (J) | chr04 | 19602852 | G | A | 98.30% | 0.00% | G -> A | NA |
LOC_Os04g32560.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g32560.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 78.343; most accessible tissue: Minghui63 flag leaf, score: 90.909 |
| vg0419603067 (J) | chr04 | 19603067 | T | TAAGTAC CTACATT CTAGTTG CAC | 58.30% | 0.36% | TAAGTACCTA CATTCTAGTT GCAC -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g32550.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.082; most accessible tissue: Callus, score: 81.227 |
| vg0419603226 (J) | chr04 | 19603226 | A | G | 98.00% | 0.00% | A -> G | NA |
LOC_Os04g32550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32560.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.577; most accessible tissue: Callus, score: 77.999 |
| vg0419603411 (J) | chr04 | 19603411 | C | T | 58.60% | 0.04% | T -> C | NA |
LOC_Os04g32550.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 63.168; most accessible tissue: Minghui63 flag leaf, score: 82.053 |
| vg0419603578 (J) | chr04 | 19603578 | A | G | 98.00% | 0.00% | A -> G | NA |
LOC_Os04g32550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.329; most accessible tissue: Minghui63 flag leaf, score: 85.327 |
| vg0419603606 (J) | chr04 | 19603606 | T | A | 51.90% | 0.00% | A -> T | NA |
LOC_Os04g32550.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.551; most accessible tissue: Minghui63 flag leaf, score: 86.000 |
| vg0419603816 (J) | chr04 | 19603816 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os04g32550.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os04g32570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g32560.1 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os04g32560.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 65.423; most accessible tissue: Minghui63 flag leaf, score: 86.159 |
| vg0419603921 (J) | chr04 | 19603921 | CAATCTT TATGTT | C | 96.20% | 0.00% | CAATCTTTAT GTT -> C | NA |
LOC_Os04g32550.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.570; most accessible tissue: Minghui63 flag leaf, score: 83.197 |
| vg0419603974 (J) | chr04 | 19603974 | AG | A | 98.00% | 0.00% | AG -> A | NA |
LOC_Os04g32550.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.420; most accessible tissue: Minghui63 flag leaf, score: 84.791 |
| vg0419604042 (J) | chr04 | 19604042 | G | A | 51.90% | 0.00% | A -> G | NA |
LOC_Os04g32550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.164; most accessible tissue: Callus, score: 82.746 |
| vg0419604065 (J) | chr04 | 19604065 | C | G | 58.40% | 0.00% | G -> C | NA |
LOC_Os04g32550.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.807; most accessible tissue: Callus, score: 82.746 |
| vg0419604089 (J) | chr04 | 19604089 | C | CA | 58.40% | 0.36% | CA -> C | NA |
LOC_Os04g32550.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 62.013; most accessible tissue: Minghui63 flag leaf, score: 79.085 |
| vg0419604188 (J) | chr04 | 19604188 | GA | GAA | 98.90% | 0.00% | GA -> GAA,G | NA |
LOC_Os04g32550.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32570.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.1 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.799; most accessible tissue: Callus, score: 83.868 |
| vg0419604462 (J) | chr04 | 19604462 | T | C | 88.50% | 0.00% | T -> C | NA |
LOC_Os04g32560.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g32560.2 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 59.185; most accessible tissue: Callus, score: 85.046 |
| vg0419604639 (J) | chr04 | 19604639 | A | G | 93.60% | 0.00% | A -> G | NA |
LOC_Os04g32550.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g32570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.282; most accessible tissue: Minghui63 flag leaf, score: 81.312 |
| vg0419604708 (J) | chr04 | 19604708 | A | G | 58.50% | 0.30% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g32550.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32560.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.699; most accessible tissue: Callus, score: 81.270 |
| vg0419604858 (J) | chr04 | 19604858 | C | T | 98.80% | 0.00% | C -> T | NA |
LOC_Os04g32560.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g32560.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 61.725; most accessible tissue: Minghui63 flag leaf, score: 83.621 |
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/