19 variations found. Os01g0699500/LOC_Os01g50410 (STE_MEKK_ste11_MAP3K.6 - STE kinases include homologs to sterile 7; sterile 11 and sterile 20 from yeast; expressed), ranging from 28,938,970 bp to 28,940,927 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g50410 | STE_MEKK_ste11_MAP3K.6 - STE kinases include homologs to sterile 7, sterile 11 and sterile 20 from yeast, expressed; RAP ID: Os01g0699500; MSU ID: LOC_Os01g50410 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os01g50410 | Os01g0699500 | MAP3K6 | MAPK KINASE KINASE6 | _ | _ |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0128939012 (J) | chr01 | 28939012 | T | C | 93.20% | 0.00% | T -> C | NA |
LOC_Os01g50410.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.572; most accessible tissue: Zhenshan97 flower, score: 99.524 |
| vg0128939153 (J) | chr01 | 28939153 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os01g50400.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g50410.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.583; most accessible tissue: Zhenshan97 flower, score: 99.436 |
| vg0128939371 (J) | chr01 | 28939371 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os01g50400.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g50410.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.725; most accessible tissue: Zhenshan97 flower, score: 99.548 |
| vg0128939385 (J) | chr01 | 28939385 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os01g50400.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g50410.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.689; most accessible tissue: Zhenshan97 flower, score: 99.548 |
| vg0128939559 (J) | chr01 | 28939559 | G | T | 99.80% | 0.00% | G -> T | NA |
LOC_Os01g50400.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g50410.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.647; most accessible tissue: Zhenshan97 flower, score: 99.338 |
| vg0128939701 (J) | chr01 | 28939701 | C | G | 58.50% | 0.00% | G -> C |
mr1013 (All); LR P-value: 3.71E-13;
mr1034 (All); LR P-value: 8.61E-13; mr1053 (All); LR P-value: 4.64E-07; mr1129 (All); LR P-value: 1.19E-35; mr1147 (All); LR P-value: 3.32E-16; mr1157 (All); LR P-value: 9.08E-07; mr1208 (All); LR P-value: 9.06E-31; mr1251 (All); LR P-value: 2.80E-26; mr1253 (All); LR P-value: 1.89E-17; mr1435 (All); LR P-value: 9.45E-37; mr1716 (All); LR P-value: 9.41E-08; mr1745 (All); LR P-value: 1.88E-34; mr1807 (All); LR P-value: 3.28E-19; mr1253_2 (All); LR P-value: 6.49E-21; mr1401_2 (All); LR P-value: 2.06E-23; mr1509_2 (All); LR P-value: 3.73E-43; mr1807_2 (All); LR P-value: 4.11E-22 |
LOC_Os01g50400.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g50410.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.771; most accessible tissue: Zhenshan97 flower, score: 99.257 |
| vg0128939759 (J) | chr01 | 28939759 | C | G | 99.80% | 0.00% | C -> G | NA |
LOC_Os01g50410.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os01g50400.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 95.127; most accessible tissue: Zhenshan97 flower, score: 99.222 |
| vg0128939788 (J) | chr01 | 28939788 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os01g50410.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.419; most accessible tissue: Zhenshan97 flower, score: 99.234 |
| vg0128939901 (J) | chr01 | 28939901 | A | T | 91.20% | 0.00% | A -> T | NA |
LOC_Os01g50410.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 94.127; most accessible tissue: Zhenshan97 flower, score: 99.254 |
| vg0128939955 (J) | chr01 | 28939955 | G | T | 95.30% | 0.00% | G -> T |
LOC_Os01g50410.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 95.627; most accessible tissue: Zhenshan97 flower, score: 99.273 |
|
| vg0128939968 (J) | chr01 | 28939968 | T | G | 87.70% | 0.00% | T -> G |
mr1409 (All); LR P-value: 4.15E-12;
mr1649 (All); LR P-value: 5.32E-12; mr1662 (All); LR P-value: 6.29E-07; mr1730 (All); LR P-value: 1.66E-09; mr1765 (All); LR P-value: 5.91E-16; mr1193_2 (All); LR P-value: 5.75E-13; mr1327_2 (All); LR P-value: 1.34E-08; mr1358_2 (Ind_All); LR P-value: 5.24E-06; mr1388_2 (All); LR P-value: 2.85E-10; mr1510_2 (All); LR P-value: 5.98E-09; mr1511_2 (All); LMM P-value: 8.57E-06; LR P-value: 3.05E-09; mr1511_2 (Ind_All); LR P-value: 4.17E-06; mr1740_2 (All); LR P-value: 2.94E-06; mr1817_2 (All); LR P-value: 4.95E-18 |
LOC_Os01g50410.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.492; most accessible tissue: Zhenshan97 flower, score: 99.211 |
| vg0128940072 (J) | chr01 | 28940072 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os01g50410.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g50400.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 95.171; most accessible tissue: Zhenshan97 flower, score: 99.040 |
| vg0128940213 (J) | chr01 | 28940213 | G | C | 58.70% | 0.00% | C -> G |
mr1013 (All); LR P-value: 2.52E-13;
mr1089 (All); LR P-value: 2.39E-42; mr1129 (All); LR P-value: 2.34E-36; mr1147 (All); LR P-value: 6.00E-16; mr1208 (All); LR P-value: 8.39E-31; mr1251 (All); LR P-value: 5.55E-27; mr1253 (All); LR P-value: 3.03E-18; mr1257 (All); LR P-value: 3.86E-31; mr1435 (All); LR P-value: 5.39E-38; mr1716 (All); LR P-value: 2.02E-07; mr1745 (All); LR P-value: 1.87E-34; mr1807 (All); LR P-value: 7.66E-20; mr1129_2 (All); LR P-value: 3.92E-36; mr1253_2 (All); LR P-value: 1.51E-21; mr1401_2 (All); LR P-value: 7.03E-24; mr1745_2 (All); LR P-value: 2.40E-38; mr1807_2 (All); LR P-value: 1.39E-22 |
LOC_Os01g50410.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 94.485; most accessible tissue: Zhenshan97 flower, score: 99.090 |
| vg0128940226 (J) | chr01 | 28940226 | A | G | 58.70% | 0.00% | G -> A |
mr1013 (All); LR P-value: 8.32E-14;
mr1053 (All); LR P-value: 8.71E-07; mr1089 (All); LR P-value: 3.25E-42; mr1129 (All); LR P-value: 3.79E-36; mr1147 (All); LR P-value: 3.05E-16; mr1157 (All); LR P-value: 7.03E-07; mr1208 (All); LR P-value: 8.44E-31; mr1251 (All); LR P-value: 6.05E-27; mr1253 (All); LR P-value: 4.47E-18; mr1257 (All); LR P-value: 1.14E-30; mr1435 (All); LR P-value: 8.15E-38; mr1716 (All); LR P-value: 2.52E-07; mr1745 (All); LR P-value: 1.41E-33; mr1807 (All); LR P-value: 2.78E-19; mr1129_2 (All); LR P-value: 6.36E-36; mr1253_2 (All); LR P-value: 1.87E-21; mr1401_2 (All); LR P-value: 1.34E-23; mr1807_2 (All); LR P-value: 2.66E-22 |
LOC_Os01g50410.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 94.348; most accessible tissue: Zhenshan97 flower, score: 98.992 |
| vg0128940311 (J) | chr01 | 28940311 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os01g50410.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 94.421; most accessible tissue: Zhenshan97 flower, score: 99.004 |
| vg0128940400 (J) | chr01 | 28940400 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os01g50410.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.520; most accessible tissue: Zhenshan97 flower, score: 99.106 |
| vg0128940445 (J) | chr01 | 28940445 | C | A | 87.50% | 0.15% | C -> A |
mr1730 (All); LR P-value: 1.74E-09;
mr1060_2 (Ind_All); LR P-value: 9.97E-06; mr1193_2 (All); LR P-value: 3.11E-12; mr1277_2 (Ind_All); LR P-value: 9.78E-06; mr1327_2 (All); LR P-value: 1.60E-08; mr1344_2 (All); LR P-value: 7.83E-06; mr1358_2 (Ind_All); LR P-value: 1.54E-06; mr1388_2 (All); LR P-value: 8.47E-10; mr1510_2 (All); LR P-value: 2.07E-09; mr1511_2 (All); LMM P-value: 5.68E-06; LR P-value: 1.94E-09; mr1511_2 (Ind_All); LMM P-value: 4.15E-06; LR P-value: 9.15E-07; mr1624_2 (Ind_All); LR P-value: 8.41E-06; mr1740_2 (All); LR P-value: 1.41E-06; mr1817_2 (All); LR P-value: 8.24E-18 |
LOC_Os01g50410.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g50410.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 95.304; most accessible tissue: Zhenshan97 flower, score: 99.248 |
| vg0128940475 (J) | chr01 | 28940475 | T | C | 58.60% | 0.00% | C -> T |
mr1013 (All); LR P-value: 1.16E-13;
mr1089 (All); LR P-value: 1.38E-41; mr1129 (All); LR P-value: 8.24E-35; mr1147 (All); LR P-value: 6.38E-17; mr1157 (All); LR P-value: 6.00E-07; mr1208 (All); LR P-value: 3.32E-29; mr1251 (All); LR P-value: 1.38E-26; mr1253 (All); LR P-value: 8.22E-18; mr1257 (All); LR P-value: 2.93E-30; mr1435 (All); LR P-value: 1.71E-36; mr1610 (All); LR P-value: 1.01E-07; mr1716 (All); LR P-value: 2.63E-07; mr1745 (All); LR P-value: 6.74E-34; mr1807 (All); LR P-value: 6.70E-20; mr1358_2 (Ind_All); LR P-value: 8.63E-06; mr1401_2 (All); LR P-value: 3.91E-23; mr1511_2 (Ind_All); LMM P-value: 5.32E-06; LR P-value: 1.33E-06; mr1807_2 (All); LR P-value: 4.88E-23; mr1807_2 (Ind_All); LR P-value: 9.93E-07 |
LOC_Os01g50410.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 95.197; most accessible tissue: Zhenshan97 flower, score: 99.167 |
| vg0128940547 (J) | chr01 | 28940547 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os01g50410.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.098; most accessible tissue: Zhenshan97 flower, score: 99.211 |
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