30 variations found. Os02g0110400/LOC_Os02g02020 (pentatricopeptide; putative; expressed), ranging from 561,822 bp to 564,487 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g02020 | pentatricopeptide, putative, expressed; RAP ID: Os02g0110400; MSU ID: LOC_Os02g02020 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0200562288 (J) | chr02 | 562288 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os02g02020.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 66.284; most accessible tissue: Callus, score: 83.585 |
| vg0200562487 (J) | chr02 | 562487 | C | T | 98.90% | 0.00% | C -> T | NA |
LOC_Os02g02020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 70.071; most accessible tissue: Callus, score: 89.178 |
| vg0200562619 (J) | chr02 | 562619 | C | T | 97.10% | 0.00% | C -> T | NA |
LOC_Os02g02020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 68.700; most accessible tissue: Zhenshan97 young leaf, score: 83.412 |
| vg0200562672 (J) | chr02 | 562672 | C | T | 60.60% | 0.00% | T -> C |
mr1680 (All); LR P-value: 3.03E-09;
mr1050_2 (All); LR P-value: 2.22E-09; mr1167_2 (All); LR P-value: 9.12E-19; mr1349_2 (All); LR P-value: 2.53E-10; mr1568_2 (All); LR P-value: 5.13E-08; mr1698_2 (All); LR P-value: 2.62E-21; mr1717_2 (All); LR P-value: 1.30E-12; mr1726_2 (All); LR P-value: 6.17E-15; mr1761_2 (All); LR P-value: 6.47E-10; mr1928_2 (Ind_All); LR P-value: 7.57E-07 |
LOC_Os02g02020.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 71.386; most accessible tissue: Zhenshan97 young leaf, score: 84.624 |
| vg0200562711 (J) | chr02 | 562711 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os02g02020.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os02g02010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.6 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.5 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 73.691; most accessible tissue: Callus, score: 89.161 |
| vg0200562733 (J) | chr02 | 562733 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os02g02020.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 73.990; most accessible tissue: Callus, score: 89.161 |
| vg0200562862 (J) | chr02 | 562862 | T | C | 89.00% | 0.00% | T -> C | NA |
LOC_Os02g02020.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 69.677; most accessible tissue: Zhenshan97 young leaf, score: 79.783 |
| vg0200562866 (J) | chr02 | 562866 | G | T | 99.60% | 0.00% | G -> T | NA |
LOC_Os02g02020.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 69.523; most accessible tissue: Zhenshan97 young leaf, score: 79.783 |
| vg0200563021 (J) | chr02 | 563021 | C | T | 98.30% | 0.00% | C -> T | NA |
LOC_Os02g02020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 76.226; most accessible tissue: Minghui63 flag leaf, score: 83.826 |
| vg0200563103 (J) | chr02 | 563103 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os02g02020.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os02g02010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.4 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.6 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.5 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.339; most accessible tissue: Minghui63 flag leaf, score: 83.412 |
| vg0200563198 (J) | chr02 | 563198 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os02g02020.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os02g02010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.4 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.6 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.5 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.473; most accessible tissue: Minghui63 flag leaf, score: 87.189 |
| vg0200563232 (J) | chr02 | 563232 | G | A | 97.10% | 0.00% | G -> A | NA |
LOC_Os02g02020.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 81.335; most accessible tissue: Minghui63 flag leaf, score: 87.326 |
| vg0200563283 (J) | chr02 | 563283 | G | T | 98.40% | 0.00% | G -> T,A | NA |
LOC_Os02g02020.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g02020.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 81.408; most accessible tissue: Minghui63 flag leaf, score: 87.461 |
| vg0200563309 (J) | chr02 | 563309 | C | T | 96.10% | 0.00% | C -> T |
LOC_Os02g02020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.410; most accessible tissue: Minghui63 flag leaf, score: 87.189 |
|
| vg0200563360 (J) | chr02 | 563360 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os02g02020.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os02g02010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.4 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.6 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.5 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.414; most accessible tissue: Minghui63 panicle, score: 89.702 |
| vg0200563399 (J) | chr02 | 563399 | C | T | 97.50% | 0.00% | C -> T | NA |
LOC_Os02g02020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.049; most accessible tissue: Minghui63 panicle, score: 90.833 |
| vg0200563471 (J) | chr02 | 563471 | C | T | 90.00% | 0.00% | C -> T |
LOC_Os02g02020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.154; most accessible tissue: Zhenshan97 panicle, score: 90.661 |
|
| vg0200563507 (J) | chr02 | 563507 | G | A | 58.80% | 0.00% | A -> G |
LOC_Os02g02020.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.258; most accessible tissue: Zhenshan97 panicle, score: 93.351 |
|
| vg0200563538 (J) | chr02 | 563538 | G | A | 96.30% | 0.00% | G -> A | NA |
LOC_Os02g02020.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 89.334; most accessible tissue: Zhenshan97 panicle, score: 93.133 |
| vg0200563579 (J) | chr02 | 563579 | A | G | 98.30% | 0.00% | A -> G | NA |
LOC_Os02g02020.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.686; most accessible tissue: Zhenshan97 panicle, score: 93.244 |
| vg0200563651 (J) | chr02 | 563651 | G | A | 69.80% | 0.00% | G -> A | NA |
LOC_Os02g02020.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.517; most accessible tissue: Zhenshan97 panicle, score: 93.936 |
| vg0200563959 (J) | chr02 | 563959 | G | T | 51.60% | 0.00% | G -> T | NA |
LOC_Os02g02020.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.900; most accessible tissue: Zhenshan97 panicle, score: 95.323 |
| vg0200564050 (J) | chr02 | 564050 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os02g02020.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os02g02010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.6 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g02040.5 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 92.491; most accessible tissue: Zhenshan97 panicle, score: 95.654 |
| vg0200564194 (J) | chr02 | 564194 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os02g02020.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.801; most accessible tissue: Zhenshan97 panicle, score: 97.376 |
| vg0200564200 (J) | chr02 | 564200 | G | A | 98.70% | 0.00% | G -> A | NA |
LOC_Os02g02020.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.783; most accessible tissue: Zhenshan97 panicle, score: 97.400 |
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