19 variations found. Os10g0400250/LOC_Os10g26070 (pentatricopeptide; putative; expressed), ranging from 13,501,850 bp to 13,503,816 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os10g26070 | pentatricopeptide, putative, expressed; RAP ID: Os10g0400250; MSU ID: LOC_Os10g26070 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1013501884 (J) | chr10 | 13501884 | A | G | 90.40% | 0.00% | A -> G |
mr1301 (All); LMM P-value: 1.15E-06; LR P-value: 2.40E-18;
mr1410 (All); LMM P-value: 1.62E-06; mr1410 (Jap_All); LR P-value: 1.98E-11; mr1533 (All); LMM P-value: 5.73E-06; mr1533 (Jap_All); LMM P-value: 8.04E-06; LR P-value: 1.65E-13; mr1871 (All); LR P-value: 1.41E-11; mr1980 (All); LMM P-value: 8.57E-10; mr1980 (Jap_All); LMM P-value: 3.88E-08; LR P-value: 2.81E-21; mr1410_2 (All); LMM P-value: 3.45E-07; LR P-value: 5.13E-15; mr1410_2 (Jap_All); LR P-value: 9.41E-12; mr1533_2 (All); LMM P-value: 6.03E-12; mr1533_2 (Jap_All); LMM P-value: 2.19E-10; LR P-value: 9.12E-25; mr1819_2 (All); LR P-value: 4.57E-08; mr1980_2 (All); LMM P-value: 8.06E-07; mr1980_2 (Jap_All); LR P-value: 5.81E-10 |
LOC_Os10g26070.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 58.040; most accessible tissue: Zhenshan97 young leaf, score: 81.353 |
| vg1013502322 (J) | chr10 | 13502322 | C | T | 98.90% | 0.00% | C -> T | NA |
LOC_Os10g26070.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 53.073; most accessible tissue: Callus, score: 75.764 |
| vg1013502325 (J) | chr10 | 13502325 | C | T | 98.90% | 0.00% | C -> T | NA |
LOC_Os10g26070.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 52.921; most accessible tissue: Callus, score: 75.764 |
| vg1013502370 (J) | chr10 | 13502370 | T | A | 99.00% | 0.00% | T -> A | NA |
LOC_Os10g26070.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 50.046; most accessible tissue: Zhenshan97 young leaf, score: 71.923 |
| vg1013502409 (J) | chr10 | 13502409 | T | A | 76.50% | 0.00% | A -> T,C |
mr1005 (All); LR P-value: 1.33E-09;
mr1022 (Jap_All); LR P-value: 3.19E-07; mr1228 (All); LR P-value: 5.31E-15; mr1275 (All); LR P-value: 1.32E-09; mr1301 (All); LMM P-value: 3.43E-06; mr1301 (Jap_All); LR P-value: 5.24E-14; mr1410 (All); LR P-value: 1.15E-14; mr1424 (All); LR P-value: 2.53E-07; mr1533 (All); LMM P-value: 2.65E-15; LR P-value: 8.99E-53; mr1533 (Jap_All); LMM P-value: 1.13E-12; LR P-value: 5.80E-22; mr1819 (All); LMM P-value: 8.98E-06; mr1881 (All); LR P-value: 4.54E-06; mr1884 (All); LR P-value: 2.23E-06; mr1980 (All); LMM P-value: 2.43E-15; LR P-value: 1.25E-48; mr1980 (Jap_All); LMM P-value: 2.92E-11; LR P-value: 2.61E-26; mr1156_2 (All); LR P-value: 4.64E-19; mr1156_2 (Jap_All); LR P-value: 9.09E-08; mr1410_2 (All); LR P-value: 1.59E-13; mr1533_2 (All); LMM P-value: 3.11E-18; LR P-value: 2.06E-55; mr1533_2 (Jap_All); LMM P-value: 3.27E-14; LR P-value: 1.49E-29; mr1980_2 (All); LMM P-value: 7.98E-12; LR P-value: 2.66E-27; mr1980_2 (Jap_All); LMM P-value: 9.62E-07; LR P-value: 3.96E-12 |
LOC_Os10g26070.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os10g26060.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g26070.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 50.648; most accessible tissue: Zhenshan97 young leaf, score: 72.340 |
| vg1013502418 (J) | chr10 | 13502418 | C | T | 93.40% | 0.00% | C -> T | NA |
LOC_Os10g26070.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 50.880; most accessible tissue: Zhenshan97 young leaf, score: 71.065 |
| vg1013502705 (J) | chr10 | 13502705 | T | C | 91.50% | 0.00% | T -> C,A |
mr1248 (All); LR P-value: 1.15E-06;
mr1301 (All); LR P-value: 1.53E-18; mr1533 (All); LMM P-value: 3.91E-07; mr1533 (Jap_All); LMM P-value: 2.40E-06; LR P-value: 3.55E-14; mr1668 (All); LR P-value: 1.32E-07; mr1699 (All); LR P-value: 1.76E-28; mr1871 (All); LR P-value: 1.85E-11; mr1980 (All); LMM P-value: 3.30E-11; mr1980 (Jap_All); LMM P-value: 1.38E-08; LR P-value: 8.81E-22; mr1410_2 (All); LR P-value: 1.60E-14; mr1533_2 (All); LMM P-value: 9.45E-13; mr1533_2 (Jap_All); LMM P-value: 8.96E-11; LR P-value: 2.47E-25; mr1819_2 (All); LR P-value: 3.39E-07; mr1980_2 (All); LMM P-value: 4.12E-07; mr1980_2 (Jap_All); LR P-value: 7.30E-10 |
LOC_Os10g26070.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g26070.1 Alt: A| missense_variant MODERATE(snpEff) LOC_Os10g26060.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 65.111; most accessible tissue: Callus, score: 81.550 |
| vg1013502769 (J) | chr10 | 13502769 | G | A | 99.50% | 0.00% | G -> A,GCGC | NA |
LOC_Os10g26070.1 Alt: GCGC| disruptive_inframe_insertion MODERATE(snpEff)
LOC_Os10g26060.1 Alt: GCGC| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g26070.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 73.121; most accessible tissue: Minghui63 flag leaf, score: 81.811 |
| vg1013502884 (J) | chr10 | 13502884 | C | T | 91.50% | 0.00% | C -> T |
mr1248 (All); LR P-value: 1.45E-06;
mr1301 (All); LR P-value: 8.97E-19; mr1533 (All); LMM P-value: 4.54E-07; mr1533 (Jap_All); LMM P-value: 2.40E-06; LR P-value: 3.55E-14; mr1668 (All); LR P-value: 5.07E-08; mr1980 (All); LMM P-value: 1.01E-11; mr1980 (Jap_All); LMM P-value: 1.38E-08; LR P-value: 8.81E-22; mr1410_2 (All); LR P-value: 1.70E-14; mr1533_2 (All); LMM P-value: 1.00E-12; mr1533_2 (Jap_All); LMM P-value: 8.96E-11; LR P-value: 2.47E-25; mr1819_2 (All); LR P-value: 7.84E-08; mr1980_2 (All); LMM P-value: 1.83E-07; mr1980_2 (Jap_All); LR P-value: 7.30E-10 |
LOC_Os10g26070.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 77.936; most accessible tissue: Zhenshan97 young leaf, score: 89.450 |
| vg1013502913 (J) | chr10 | 13502913 | T | C | 66.80% | 0.00% | C -> T | NA |
LOC_Os10g26070.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 81.703; most accessible tissue: Zhenshan97 young leaf, score: 90.547 |
| vg1013502982 (J) | chr10 | 13502982 | T | C | 66.80% | 0.00% | C -> T | NA |
LOC_Os10g26070.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.704; most accessible tissue: Zhenshan97 young leaf, score: 92.535 |
| vg1013503093 (J) | chr10 | 13503093 | G | A | 75.40% | 0.00% | A -> G |
mr1005 (All); LR P-value: 1.13E-09;
mr1022 (Jap_All); LR P-value: 3.19E-07; mr1228 (All); LR P-value: 3.37E-15; mr1275 (All); LR P-value: 2.43E-09; mr1301 (All); LMM P-value: 9.23E-07; mr1301 (Jap_All); LR P-value: 5.24E-14; mr1364 (All); LR P-value: 1.73E-07; mr1410 (All); LMM P-value: 6.48E-06; LR P-value: 3.95E-15; mr1424 (All); LR P-value: 4.03E-07; mr1443 (All); LR P-value: 8.53E-07; mr1533 (All); LMM P-value: 8.64E-16; LR P-value: 6.82E-53; mr1533 (Jap_All); LMM P-value: 1.13E-12; LR P-value: 5.80E-22; mr1681 (All); LR P-value: 7.46E-06; mr1884 (All); LR P-value: 3.96E-06; mr1980 (All); LMM P-value: 2.23E-16; LR P-value: 2.08E-49; mr1980 (Jap_All); LMM P-value: 2.92E-11; LR P-value: 2.61E-26; mr1156_2 (All); LR P-value: 6.77E-19; mr1156_2 (Jap_All); LR P-value: 9.09E-08; mr1410_2 (All); LR P-value: 8.16E-14; mr1533_2 (All); LMM P-value: 1.13E-18; LR P-value: 3.28E-55; mr1533_2 (Jap_All); LMM P-value: 3.27E-14; LR P-value: 1.49E-29; mr1645_2 (All); LR P-value: 1.03E-07; mr1980_2 (All); LMM P-value: 2.22E-12; LR P-value: 1.27E-27; mr1980_2 (Jap_All); LMM P-value: 9.62E-07; LR P-value: 3.96E-12 |
LOC_Os10g26070.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.004; most accessible tissue: Zhenshan97 flag leaf, score: 96.910 |
| vg1013503122 (J) | chr10 | 13503122 | C | T | 85.50% | 0.25% | C -> T |
mr1533 (All); LMM P-value: 3.79E-20;
mr1533 (Ind_All); LMM P-value: 5.46E-21; LR P-value: 5.40E-28; mr1667 (Ind_All); LR P-value: 7.68E-06; mr1980 (All); LMM P-value: 2.60E-23; mr1980 (Ind_All); LMM P-value: 2.07E-24; LR P-value: 4.65E-31; mr1533_2 (All); LMM P-value: 2.27E-21; mr1533_2 (Ind_All); LMM P-value: 4.63E-24; LR P-value: 8.07E-35; mr1980_2 (All); LMM P-value: 1.31E-07; mr1980_2 (Ind_All); LMM P-value: 1.01E-07; LR P-value: 5.03E-12 |
LOC_Os10g26070.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g26070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 90.868; most accessible tissue: Zhenshan97 flag leaf, score: 97.600 |
| vg1013503139 (J) | chr10 | 13503139 | A | G | 98.90% | 0.00% | A -> G | NA |
LOC_Os10g26070.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 90.783; most accessible tissue: Zhenshan97 flag leaf, score: 97.589 |
| vg1013503300 (J) | chr10 | 13503300 | G | T | 56.40% | 0.32% | G -> T |
mr1457 (All); LR P-value: 4.31E-11;
mr1533 (All); LMM P-value: 2.04E-20; LR P-value: 2.99E-39; mr1533 (Ind_All); LMM P-value: 1.41E-20; LR P-value: 4.94E-28; mr1667 (Ind_All); LR P-value: 4.64E-06; mr1980 (All); LMM P-value: 1.01E-22; LR P-value: 1.57E-38; mr1980 (Ind_All); LMM P-value: 3.16E-24; LR P-value: 7.33E-33; mr1533_2 (All); LMM P-value: 1.40E-20; LR P-value: 3.94E-43; mr1533_2 (Ind_All); LMM P-value: 1.03E-23; LR P-value: 2.48E-35; mr1980_2 (All); LMM P-value: 6.57E-09; LR P-value: 2.93E-18; mr1980_2 (Ind_All); LMM P-value: 6.82E-09; LR P-value: 1.40E-13 |
LOC_Os10g26070.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g26070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 94.428; most accessible tissue: Zhenshan97 flag leaf, score: 98.663 |
| vg1013503362 (J) | chr10 | 13503362 | C | A | 91.50% | 0.00% | C -> A |
mr1248 (All); LR P-value: 1.15E-06;
mr1301 (All); LR P-value: 1.53E-18; mr1533 (All); LMM P-value: 3.91E-07; mr1533 (Jap_All); LMM P-value: 2.40E-06; LR P-value: 3.55E-14; mr1668 (All); LR P-value: 1.32E-07; mr1699 (All); LR P-value: 1.76E-28; mr1871 (All); LR P-value: 1.85E-11; mr1980 (All); LMM P-value: 3.30E-11; mr1980 (Jap_All); LMM P-value: 1.38E-08; LR P-value: 8.81E-22; mr1410_2 (All); LR P-value: 1.60E-14; mr1533_2 (All); LMM P-value: 9.45E-13; mr1533_2 (Jap_All); LMM P-value: 8.96E-11; LR P-value: 2.47E-25; mr1819_2 (All); LR P-value: 3.39E-07; mr1980_2 (All); LMM P-value: 4.12E-07; mr1980_2 (Jap_All); LR P-value: 7.30E-10 |
LOC_Os10g26070.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.807; most accessible tissue: Zhenshan97 flag leaf, score: 98.590 |
| vg1013503414 (J) | chr10 | 13503414 | A | C | 66.80% | 0.00% | C -> A,G | NA |
LOC_Os10g26070.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os10g26060.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g26070.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 92.043; most accessible tissue: Zhenshan97 flag leaf, score: 98.762 |
| vg1013503688 (J) | chr10 | 13503688 | C | T | 75.30% | 0.00% | T -> C |
mr1005 (All); LR P-value: 7.29E-10;
mr1022 (Jap_All); LR P-value: 3.19E-07; mr1228 (All); LR P-value: 2.21E-15; mr1275 (All); LR P-value: 9.90E-10; mr1301 (All); LMM P-value: 1.22E-06; mr1301 (Jap_All); LR P-value: 5.24E-14; mr1376 (All); LR P-value: 8.30E-14; mr1410 (All); LR P-value: 2.63E-14; mr1424 (All); LR P-value: 7.60E-08; mr1431 (All); LR P-value: 8.30E-14; mr1450 (All); LR P-value: 3.63E-06; mr1533 (All); LMM P-value: 2.21E-15; LR P-value: 9.17E-53; mr1533 (Jap_All); LMM P-value: 1.13E-12; LR P-value: 5.80E-22; mr1575 (All); LR P-value: 1.00E-08; mr1819 (All); LMM P-value: 6.11E-06; mr1884 (All); LR P-value: 1.39E-06; mr1980 (All); LMM P-value: 1.05E-15; LR P-value: 1.15E-48; mr1980 (Jap_All); LMM P-value: 2.92E-11; LR P-value: 2.61E-26; mr1156_2 (All); LR P-value: 3.05E-20; mr1156_2 (Jap_All); LR P-value: 9.09E-08; mr1533_2 (All); LMM P-value: 1.84E-17; LR P-value: 8.16E-54; mr1533_2 (Jap_All); LMM P-value: 3.27E-14; LR P-value: 1.49E-29; mr1980_2 (All); LMM P-value: 1.37E-11; LR P-value: 6.02E-27; mr1980_2 (Jap_All); LMM P-value: 9.62E-07; LR P-value: 3.96E-12 |
LOC_Os10g26070.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 97.523; most accessible tissue: Zhenshan97 flag leaf, score: 98.797 |
| vg1013503690 (J) | chr10 | 13503690 | A | G | 98.90% | 0.00% | A -> G | NA |
LOC_Os10g26070.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 97.595; most accessible tissue: Zhenshan97 flag leaf, score: 98.846 |