17 variations found. Os10g0484300/LOC_Os10g34310 (PPR repeat containing protein; expressed), ranging from 18,297,832 bp to 18,300,228 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os10g34310 | PPR repeat containing protein, expressed; RAP ID: Os10g0484300; MSU ID: LOC_Os10g34310 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1018297861 (J) | chr10 | 18297861 | G | GT | 85.60% | 0.28% | G -> GT,GTT | NA |
LOC_Os10g34310.1 Alt: GTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g34310.2 Alt: GTT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34300.1 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34290.1 Alt: GTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34320.1 Alt: GTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34310.1 Alt: GT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34310.2 Alt: GT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34300.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34290.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34320.1 Alt: GT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 56.009; most accessible tissue: Zhenshan97 flower, score: 73.414 |
| vg1018297998 (J) | chr10 | 18297998 | A | C | 96.30% | 0.00% | A -> C | NA |
LOC_Os10g34310.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g34310.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34300.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34290.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34320.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.246; most accessible tissue: Callus, score: 91.645 |
| vg1018298010 (J) | chr10 | 18298010 | A | T | 56.10% | 0.06% | T -> A |
mr1016 (Jap_All); LR P-value: 1.11E-12;
mr1017 (Jap_All); LR P-value: 5.44E-12; mr1018 (Jap_All); LR P-value: 8.94E-11; mr1019 (Jap_All); LR P-value: 1.66E-08; mr1055 (Jap_All); LR P-value: 6.52E-14; mr1129 (Jap_All); LR P-value: 1.99E-08; mr1132 (Jap_All); LR P-value: 9.17E-11; mr1178 (Jap_All); LR P-value: 1.06E-10; mr1390 (Jap_All); LR P-value: 5.23E-12; mr1490 (Jap_All); LR P-value: 7.68E-12; mr1771 (Jap_All); LR P-value: 7.44E-15; mr1019_2 (Jap_All); LR P-value: 6.79E-12; mr1022_2 (Jap_All); LR P-value: 4.15E-09; mr1055_2 (Jap_All); LMM P-value: 9.29E-06; LR P-value: 2.38E-15; mr1132_2 (Jap_All); LMM P-value: 3.71E-06; LR P-value: 1.12E-16; mr1178_2 (Jap_All); LR P-value: 7.26E-18; mr1261_2 (Jap_All); LR P-value: 2.74E-09; mr1390_2 (Jap_All); LR P-value: 8.92E-16; mr1490_2 (Jap_All); LR P-value: 1.18E-16; mr1632_2 (Jap_All); LR P-value: 6.35E-07 |
LOC_Os10g34310.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g34310.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34290.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34320.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 50.446; most accessible tissue: Callus, score: 91.645 |
| vg1018298206 (J) | chr10 | 18298206 | G | A | 96.30% | 0.00% | G -> A | NA |
LOC_Os10g34310.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g34310.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34290.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34320.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 47.846; most accessible tissue: Callus, score: 89.954 |
| vg1018298987 (J) | chr10 | 18298987 | C | A | 73.20% | 0.00% | A -> C |
mr1016 (Jap_All); LR P-value: 1.11E-12;
mr1017 (Jap_All); LR P-value: 5.44E-12; mr1018 (Jap_All); LR P-value: 8.94E-11; mr1019 (All); LR P-value: 6.06E-56; mr1019 (Jap_All); LR P-value: 1.66E-08; mr1055 (All); LMM P-value: 9.73E-06; mr1055 (Jap_All); LR P-value: 6.52E-14; mr1129 (Jap_All); LR P-value: 1.99E-08; mr1132 (Jap_All); LR P-value: 9.17E-11; mr1178 (Jap_All); LR P-value: 1.06E-10; mr1390 (Jap_All); LR P-value: 5.23E-12; mr1490 (Jap_All); LR P-value: 7.68E-12; mr1630 (All); LR P-value: 1.46E-10; mr1691 (All); LR P-value: 4.56E-09; mr1693 (All); LR P-value: 8.94E-09; mr1771 (All); LMM P-value: 2.29E-08; LR P-value: 1.72E-50; mr1771 (Jap_All); LR P-value: 7.44E-15; mr1784 (All); LR P-value: 1.50E-42; mr1862 (All); LR P-value: 1.43E-26; mr1019_2 (Jap_All); LR P-value: 6.79E-12; mr1022_2 (Jap_All); LR P-value: 4.15E-09; mr1023_2 (All); LMM P-value: 2.78E-06; mr1055_2 (All); LMM P-value: 7.03E-06; mr1055_2 (Jap_All); LMM P-value: 9.29E-06; LR P-value: 2.38E-15; mr1132_2 (All); LMM P-value: 4.08E-08; mr1132_2 (Jap_All); LMM P-value: 3.71E-06; LR P-value: 1.12E-16; mr1178_2 (Jap_All); LR P-value: 7.26E-18; mr1217_2 (All); LR P-value: 3.78E-13; mr1261_2 (Jap_All); LR P-value: 2.74E-09; mr1390_2 (Jap_All); LR P-value: 8.92E-16; mr1490_2 (Jap_All); LR P-value: 1.18E-16; mr1632_2 (Jap_All); LR P-value: 6.35E-07; mr1771_2 (All); LR P-value: 1.41E-45; mr1784_2 (All); LR P-value: 5.66E-46; mr1862_2 (All); LR P-value: 3.50E-42 |
LOC_Os10g34310.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os10g34310.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 64.376; most accessible tissue: Callus, score: 85.176 |
| vg1018299002 (J) | chr10 | 18299002 | G | T | 73.10% | 0.00% | T -> G |
mr1016 (Jap_All); LR P-value: 1.24E-12;
mr1017 (Jap_All); LR P-value: 5.42E-12; mr1018 (Jap_All); LR P-value: 8.91E-11; mr1019 (Jap_All); LR P-value: 1.90E-08; mr1055 (Jap_All); LR P-value: 9.15E-14; mr1129 (Jap_All); LR P-value: 1.83E-08; mr1132 (Jap_All); LR P-value: 1.07E-10; mr1178 (Jap_All); LR P-value: 1.60E-10; mr1271 (Jap_All); LR P-value: 8.27E-07; mr1390 (Jap_All); LR P-value: 6.57E-12; mr1435 (Jap_All); LR P-value: 2.37E-10; mr1490 (Jap_All); LR P-value: 1.02E-11; mr1630 (All); LR P-value: 1.24E-10; mr1691 (All); LR P-value: 3.94E-09; mr1693 (All); LR P-value: 8.18E-09; mr1771 (All); LMM P-value: 1.15E-08; LR P-value: 4.17E-51; mr1771 (Jap_All); LR P-value: 3.85E-15; mr1784 (All); LMM P-value: 9.21E-06; LR P-value: 6.29E-43; mr1862 (All); LMM P-value: 5.69E-06; LR P-value: 4.94E-27; mr1019_2 (Jap_All); LR P-value: 7.41E-12; mr1022_2 (Jap_All); LR P-value: 4.12E-09; mr1023_2 (All); LMM P-value: 9.47E-06; mr1055_2 (Jap_All); LR P-value: 3.46E-15; mr1132_2 (All); LMM P-value: 4.00E-07; mr1132_2 (Jap_All); LMM P-value: 5.58E-06; LR P-value: 1.35E-16; mr1178_2 (Jap_All); LR P-value: 1.37E-17; mr1217_2 (All); LR P-value: 1.66E-13; mr1261_2 (Jap_All); LR P-value: 2.62E-09; mr1390_2 (Jap_All); LR P-value: 1.08E-15; mr1490_2 (Jap_All); LR P-value: 1.52E-16; mr1632_2 (Jap_All); LR P-value: 5.89E-07; mr1771_2 (All); LR P-value: 1.86E-45; mr1784_2 (All); LR P-value: 4.14E-46; mr1862_2 (All); LR P-value: 3.65E-42; mr1862_2 (Jap_All); LR P-value: 1.90E-08 |
LOC_Os10g34310.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g34310.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 64.901; most accessible tissue: Callus, score: 85.176 |
| vg1018299226 (J) | chr10 | 18299226 | G | A | 73.20% | 0.00% | A -> G |
mr1016 (Jap_All); LR P-value: 1.11E-12;
mr1017 (Jap_All); LR P-value: 5.44E-12; mr1018 (Jap_All); LR P-value: 8.94E-11; mr1019 (All); LR P-value: 3.62E-56; mr1019 (Jap_All); LR P-value: 1.66E-08; mr1055 (All); LMM P-value: 4.50E-06; mr1055 (Jap_All); LR P-value: 6.52E-14; mr1129 (Jap_All); LR P-value: 1.99E-08; mr1132 (Jap_All); LR P-value: 9.17E-11; mr1178 (Jap_All); LR P-value: 1.06E-10; mr1390 (Jap_All); LR P-value: 5.23E-12; mr1490 (Jap_All); LR P-value: 7.68E-12; mr1630 (All); LR P-value: 2.13E-10; mr1691 (All); LR P-value: 7.15E-09; mr1693 (All); LR P-value: 7.49E-09; mr1771 (All); LMM P-value: 2.62E-07; LR P-value: 2.83E-49; mr1771 (Jap_All); LR P-value: 7.44E-15; mr1784 (All); LR P-value: 7.24E-42; mr1862 (All); LR P-value: 2.41E-26; mr1019_2 (Jap_All); LR P-value: 6.79E-12; mr1022_2 (Jap_All); LR P-value: 4.15E-09; mr1023_2 (All); LMM P-value: 1.55E-06; mr1055_2 (All); LMM P-value: 3.19E-06; mr1055_2 (Jap_All); LMM P-value: 9.29E-06; LR P-value: 2.38E-15; mr1132_2 (All); LMM P-value: 1.76E-08; mr1132_2 (Jap_All); LMM P-value: 3.71E-06; LR P-value: 1.12E-16; mr1178_2 (All); LMM P-value: 9.54E-06; mr1178_2 (Jap_All); LR P-value: 7.26E-18; mr1217_2 (All); LR P-value: 2.01E-13; mr1261_2 (Jap_All); LR P-value: 2.74E-09; mr1390_2 (All); LMM P-value: 8.95E-06; mr1390_2 (Jap_All); LR P-value: 8.92E-16; mr1489_2 (All); LMM P-value: 7.91E-06; mr1490_2 (Jap_All); LR P-value: 1.18E-16; mr1632_2 (Jap_All); LR P-value: 6.35E-07; mr1771_2 (All); LR P-value: 2.54E-45; mr1778_2 (All); LMM P-value: 6.32E-06; mr1784_2 (All); LR P-value: 1.31E-45; mr1862_2 (All); LR P-value: 1.77E-41 |
LOC_Os10g34310.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g34310.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 70.998; most accessible tissue: Callus, score: 87.845 |
| vg1018299271 (J) | chr10 | 18299271 | C | T | 73.10% | 0.02% | T -> C |
mr1016 (Jap_All); LR P-value: 1.11E-12;
mr1017 (Jap_All); LR P-value: 5.44E-12; mr1018 (Jap_All); LR P-value: 8.94E-11; mr1019 (All); LR P-value: 6.06E-56; mr1019 (Jap_All); LR P-value: 1.66E-08; mr1055 (All); LMM P-value: 9.73E-06; mr1055 (Jap_All); LR P-value: 6.52E-14; mr1129 (Jap_All); LR P-value: 1.99E-08; mr1132 (Jap_All); LR P-value: 9.17E-11; mr1178 (Jap_All); LR P-value: 1.06E-10; mr1390 (Jap_All); LR P-value: 5.23E-12; mr1490 (Jap_All); LR P-value: 7.68E-12; mr1630 (All); LR P-value: 1.46E-10; mr1691 (All); LR P-value: 4.56E-09; mr1693 (All); LR P-value: 8.94E-09; mr1771 (All); LMM P-value: 2.29E-08; LR P-value: 1.72E-50; mr1771 (Jap_All); LR P-value: 7.44E-15; mr1784 (All); LR P-value: 1.50E-42; mr1862 (All); LR P-value: 1.43E-26; mr1019_2 (Jap_All); LR P-value: 6.79E-12; mr1022_2 (Jap_All); LR P-value: 4.15E-09; mr1023_2 (All); LMM P-value: 2.78E-06; mr1055_2 (All); LMM P-value: 7.03E-06; mr1055_2 (Jap_All); LMM P-value: 9.29E-06; LR P-value: 2.38E-15; mr1132_2 (All); LMM P-value: 4.08E-08; mr1132_2 (Jap_All); LMM P-value: 3.71E-06; LR P-value: 1.12E-16; mr1178_2 (Jap_All); LR P-value: 7.26E-18; mr1217_2 (All); LR P-value: 3.78E-13; mr1261_2 (Jap_All); LR P-value: 2.74E-09; mr1390_2 (Jap_All); LR P-value: 8.92E-16; mr1490_2 (Jap_All); LR P-value: 1.18E-16; mr1632_2 (Jap_All); LR P-value: 6.35E-07; mr1771_2 (All); LR P-value: 1.41E-45; mr1784_2 (All); LR P-value: 5.66E-46; mr1862_2 (All); LR P-value: 3.50E-42 |
LOC_Os10g34310.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g34310.2 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os10g34310.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os10g34310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 79.982; most accessible tissue: Callus, score: 87.845 |
| vg1018299272 (J) | chr10 | 18299272 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os10g34310.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os10g34310.2 Alt: A| missense_variant MODERATE(snpEff) LOC_Os10g34300.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g34320.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.982; most accessible tissue: Callus, score: 87.845 |
| vg1018299521 (J) | chr10 | 18299521 | C | T | 85.60% | 0.00% | C -> T |
LOC_Os10g34310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os10g34310.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 88.052; most accessible tissue: Zhenshan97 flag leaf, score: 92.520 |
|
| vg1018299597 (J) | chr10 | 18299597 | C | T | 91.60% | 0.00% | C -> T |
LOC_Os10g34310.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g34310.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 88.065; most accessible tissue: Zhenshan97 flag leaf, score: 95.424 |
|
| vg1018299804 (J) | chr10 | 18299804 | C | A | 83.20% | 0.17% | C -> A | NA |
LOC_Os10g34310.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g34310.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os10g34310.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os10g34310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 92.356; most accessible tissue: Zhenshan97 flag leaf, score: 96.879 |
| vg1018299867 (J) | chr10 | 18299867 | G | C | 98.00% | 0.00% | G -> C | NA |
LOC_Os10g34310.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os10g34310.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 90.345; most accessible tissue: Zhenshan97 flag leaf, score: 96.743 |
| vg1018299880 (J) | chr10 | 18299880 | A | C | 52.20% | 0.04% | C -> A |
LOC_Os10g34310.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g34310.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os10g34310.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os10g34310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 90.411; most accessible tissue: Zhenshan97 flag leaf, score: 96.718 |
|
| vg1018300070 (J) | chr10 | 18300070 | C | A | 68.30% | 2.33% | A -> C | NA |
LOC_Os10g34310.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os10g34310.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os10g34310.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os10g34310.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 92.645; most accessible tissue: Zhenshan97 flag leaf, score: 96.432 |
| vg1018300102 (J) | chr10 | 18300102 | C | T | 97.90% | 0.00% | C -> T | NA |
LOC_Os10g34310.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os10g34310.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 92.000; most accessible tissue: Zhenshan97 flag leaf, score: 96.488 |
| vg1018300164 (J) | chr10 | 18300164 | GTTCTTT TCAGGAC T | G | 62.40% | 0.04% | GTTCTTTTCA GGACT -> G | NA |
LOC_Os10g34310.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g34300.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34310.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34330.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g34320.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 91.243; most accessible tissue: Zhenshan97 flag leaf, score: 95.601 |