127 variations found. Os01g0359600/LOC_Os01g25740 (powdery mildew resistance protein PM3F; putative; expressed), ranging from 14,587,006 bp to 14,591,754 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g25740 | powdery mildew resistance protein PM3F, putative, expressed; RAP ID: Os01g0359600; MSU ID: LOC_Os01g25740 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0114587033 (J) | chr01 | 14587033 | GT | G | 74.80% | 20.59% | GT -> G | NA |
LOC_Os01g25740.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g25730.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 57.243; most accessible tissue: Zhenshan97 young leaf, score: 71.497 |
| vg0114587042 (J) | chr01 | 14587042 | ATC | A | 79.20% | 20.23% | ATC -> A | NA |
LOC_Os01g25740.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g25730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 59.556; most accessible tissue: Zhenshan97 young leaf, score: 73.147 |
| vg0114587052 (J) | chr01 | 14587052 | C | T | 78.50% | 20.08% | C -> T | NA |
LOC_Os01g25740.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g25730.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 59.295; most accessible tissue: Zhenshan97 young leaf, score: 72.340 |
| vg0114587058 (J) | chr01 | 14587058 | C | A | 63.90% | 21.29% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25740.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25730.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.369; most accessible tissue: Zhenshan97 young leaf, score: 71.923 |
| vg0114587113 (J) | chr01 | 14587113 | CAAACAA GACTTTA GT | C | 61.40% | 31.74% | CAAACAAGAC TTTAGT -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25740.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25730.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.793; most accessible tissue: Zhenshan97 young leaf, score: 76.440 |
| vg0114587117 (J) | chr01 | 14587117 | C | CA | 64.90% | 20.52% | C -> CA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25740.1 Alt: CA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25730.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.793; most accessible tissue: Zhenshan97 young leaf, score: 76.440 |
| vg0114587149 (J) | chr01 | 14587149 | T | C | 78.50% | 20.12% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25740.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25730.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.009; most accessible tissue: Zhenshan97 young leaf, score: 75.751 |
| vg0114587154 (J) | chr01 | 14587154 | G | T | 44.70% | 21.05% | T -> G |
mr1072 (All); LR P-value: 5.55E-28;
mr1075 (All); LR P-value: 2.70E-28; mr1194 (All); LR P-value: 1.22E-43; mr1202 (All); LR P-value: 3.06E-30; mr1222 (All); LR P-value: 4.54E-08; mr1653 (All); LR P-value: 3.21E-14; mr1672 (Ind_All); LMM P-value: 4.32E-06; LR P-value: 6.52E-07; mr1072_2 (All); LMM P-value: 4.63E-06; LR P-value: 1.80E-41; mr1075_2 (All); LMM P-value: 6.85E-06; LR P-value: 3.17E-41; mr1124_2 (All); LR P-value: 2.18E-56; mr1124_2 (Ind_All); LR P-value: 2.22E-09; mr1222_2 (All); LR P-value: 1.87E-09; mr1519_2 (All); LMM P-value: 9.67E-06; LR P-value: 1.06E-45; mr1592_2 (All); LR P-value: 2.53E-17; mr1600_2 (All); LR P-value: 1.15E-08; mr1712_2 (All); LR P-value: 6.52E-17; mr1722_2 (All); LR P-value: 1.54E-11; mr1748_2 (All); LR P-value: 1.77E-07; mr1749_2 (All); LR P-value: 6.90E-08; mr1821_2 (All); LR P-value: 2.85E-07; mr1861_2 (All); LR P-value: 4.75E-48 |
LOC_Os01g25740.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g25730.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 62.493; most accessible tissue: Zhenshan97 young leaf, score: 75.751 |
| vg0114587164 (J) | chr01 | 14587164 | C | G | 65.00% | 20.55% | C -> G | NA |
LOC_Os01g25740.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g25730.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 61.780; most accessible tissue: Zhenshan97 young leaf, score: 75.397 |
| vg0114587216 (J) | chr01 | 14587216 | G | A | 60.70% | 20.69% | G -> A |
LOC_Os01g25740.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g25730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 60.201; most accessible tissue: Callus, score: 73.987 |
|
| vg0114587310 (J) | chr01 | 14587310 | T | C | 78.70% | 19.40% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25730.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25740.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.347; most accessible tissue: Zhenshan97 young leaf, score: 78.644 |
| vg0114587391 (J) | chr01 | 14587391 | CT | C | 59.40% | 21.84% | CT -> C,CTT,TT | NA |
LOC_Os01g25730.1 Alt: TT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g25740.1 Alt: TT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25730.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25740.1 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g25730.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25740.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.425; most accessible tissue: Zhenshan97 young leaf, score: 79.783 |
| vg0114587401 (J) | chr01 | 14587401 | T | TC | 60.70% | 20.82% | T -> TC,C,TTC | NA |
LOC_Os01g25730.1 Alt: TC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g25740.1 Alt: TC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g25730.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25740.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25730.1 Alt: TTC| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g25740.1 Alt: TTC| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 62.997; most accessible tissue: Zhenshan97 young leaf, score: 78.347 |
| vg0114587405 (J) | chr01 | 14587405 | G | T | 77.80% | 19.72% | G -> T | NA |
LOC_Os01g25730.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g25740.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 62.957; most accessible tissue: Zhenshan97 young leaf, score: 78.644 |
| vg0114587466 (J) | chr01 | 14587466 | G | T | 78.10% | 19.78% | G -> T | NA |
LOC_Os01g25730.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g25740.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 63.825; most accessible tissue: Zhenshan97 young leaf, score: 78.644 |
| vg0114587475 (J) | chr01 | 14587475 | T | C | 75.20% | 19.87% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25730.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25740.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.132; most accessible tissue: Zhenshan97 young leaf, score: 76.099 |
| vg0114587493 (J) | chr01 | 14587493 | C | CAA | 77.90% | 19.72% | C -> CAA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25730.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25740.1 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.395; most accessible tissue: Zhenshan97 young leaf, score: 77.101 |
| vg0114587495 (J) | chr01 | 14587495 | C | T | 77.90% | 19.70% | C -> T | NA |
LOC_Os01g25730.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g25740.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 62.395; most accessible tissue: Zhenshan97 young leaf, score: 77.101 |
| vg0114587506 (J) | chr01 | 14587506 | G | A | 78.70% | 19.95% | G -> A | NA |
LOC_Os01g25730.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g25740.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 62.436; most accessible tissue: Zhenshan97 young leaf, score: 77.422 |
| vg0114587514 (J) | chr01 | 14587514 | C | T | 60.70% | 20.72% | C -> T |
LOC_Os01g25740.1 Alt: T| splice_donor_variant&intron_variant HIGH(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 63.741; most accessible tissue: Zhenshan97 young leaf, score: 78.644 |
|
| vg0114587575 (J) | chr01 | 14587575 | C | T | 79.60% | 16.63% | C -> T | NA |
LOC_Os01g25740.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g25740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 64.553; most accessible tissue: Zhenshan97 young leaf, score: 79.783 |
| vg0114587589 (J) | chr01 | 14587589 | T | A | 78.00% | 17.10% | T -> A |
LOC_Os01g25740.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g25740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 63.028; most accessible tissue: Zhenshan97 young leaf, score: 81.102 |
|
| vg0114587626 (J) | chr01 | 14587626 | G | T | 79.40% | 18.96% | G -> T | NA |
LOC_Os01g25740.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g25740.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 63.133; most accessible tissue: Zhenshan97 young leaf, score: 80.325 |
| vg0114587683 (J) | chr01 | 14587683 | G | C | 81.20% | 16.46% | G -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25730.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25740.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.085; most accessible tissue: Zhenshan97 young leaf, score: 80.589 |
| vg0114587699 (J) | chr01 | 14587699 | T | C | 78.50% | 16.50% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g25730.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g25740.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.823; most accessible tissue: Zhenshan97 young leaf, score: 78.044 |
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