281 variations found. Os02g0555900/LOC_Os02g35010 (STE_MEKK_ste11_MAP3K.9 - STE kinases include homologs to sterile 7; sterile 11 and sterile 20 from yeast; expressed), ranging from 21,002,128 bp to 21,008,409 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g35010 | STE_MEKK_ste11_MAP3K.9 - STE kinases include homologs to sterile 7, sterile 11 and sterile 20 from yeast, expressed; RAP ID: Os02g0555900; MSU ID: LOC_Os02g35010 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0221002372 (J) | chr02 | 21002372 | CTCTC | C | 98.30% | 0.00% | CTCTC -> C | NA |
|
| STR0221002421 (J) | chr02 | 21002421 | CAGATCA GATCAGA TCAGA | CAGATCA GATCAGA | 63.70% | 0.00% | CAGATCAGAT CAGA -> CAGATCAGAT CAGATCAGA | NA |
|
| STR0221005183 (J) | chr02 | 21005183 | AAAAAA | AAAAA | 51.00% | 0.00% | AAAAAA -> AAAAA | NA |
|
| STR0221005469 (J) | chr02 | 21005469 | AATAAAA ATAAATT G | AATAAAA AATAAAT TT | 45.30% | 0.00% | AATAAAAATA AATTG -> AATAAAAAAT AAATTT | NA |
|
| STR0221005815 (J) | chr02 | 21005815 | CCT | C | 97.90% | 0.00% | CCT -> C | NA |
|
| vg0221002132 (J) | chr02 | 21002132 | C | A | 66.40% | 0.00% | A -> C |
mr1014 (All); LR P-value: 4.80E-69;
mr1101 (Jap_All); LMM P-value: 6.12E-07; mr1116 (All); LR P-value: 1.17E-16; mr1134 (All); LR P-value: 7.81E-81; mr1135 (All); LR P-value: 2.30E-74; mr1168 (All); LR P-value: 2.35E-21; mr1242 (All); LR P-value: 4.00E-20; mr1383 (All); LR P-value: 3.98E-24; mr1504 (All); LR P-value: 3.21E-87; mr1510 (All); LR P-value: 7.85E-07; mr1595 (All); LR P-value: 9.06E-10; mr1645 (All); LR P-value: 1.23E-39; mr1647 (All); LR P-value: 8.75E-33; mr1670 (All); LR P-value: 1.05E-33; mr1682 (All); LR P-value: 2.93E-37; mr1698 (All); LR P-value: 4.48E-22; mr1717 (Jap_All); LMM P-value: 8.72E-06; LR P-value: 8.72E-06; mr1754 (All); LR P-value: 1.08E-21; mr1767 (All); LR P-value: 1.32E-18; mr1917 (All); LR P-value: 9.70E-26; mr1987 (All); LR P-value: 4.20E-101; mr1128_2 (All); LR P-value: 1.75E-12; mr1148_2 (All); LR P-value: 2.17E-15; mr1150_2 (All); LR P-value: 4.79E-31; mr1242_2 (All); LR P-value: 5.02E-24; mr1657_2 (All); LR P-value: 2.78E-18; mr1698_2 (All); LR P-value: 6.28E-22 |
LOC_Os02g35010.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35000.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.077; most accessible tissue: Minghui63 flag leaf, score: 90.086 |
| vg0221002142 (J) | chr02 | 21002142 | T | C | 66.30% | 0.00% | C -> T |
mr1014 (All); LR P-value: 4.80E-69;
mr1101 (Jap_All); LMM P-value: 6.12E-07; mr1116 (All); LR P-value: 1.17E-16; mr1134 (All); LR P-value: 7.81E-81; mr1135 (All); LR P-value: 2.30E-74; mr1168 (All); LR P-value: 2.35E-21; mr1242 (All); LR P-value: 4.00E-20; mr1383 (All); LR P-value: 3.98E-24; mr1504 (All); LR P-value: 3.21E-87; mr1510 (All); LR P-value: 7.85E-07; mr1595 (All); LR P-value: 9.06E-10; mr1645 (All); LR P-value: 1.23E-39; mr1647 (All); LR P-value: 8.75E-33; mr1670 (All); LR P-value: 1.05E-33; mr1682 (All); LR P-value: 2.93E-37; mr1698 (All); LR P-value: 4.48E-22; mr1717 (Jap_All); LMM P-value: 8.72E-06; LR P-value: 8.72E-06; mr1754 (All); LR P-value: 1.08E-21; mr1767 (All); LR P-value: 1.32E-18; mr1917 (All); LR P-value: 9.70E-26; mr1987 (All); LR P-value: 4.20E-101; mr1128_2 (All); LR P-value: 1.75E-12; mr1148_2 (All); LR P-value: 2.17E-15; mr1150_2 (All); LR P-value: 4.79E-31; mr1242_2 (All); LR P-value: 5.02E-24; mr1657_2 (All); LR P-value: 2.78E-18; mr1698_2 (All); LR P-value: 6.28E-22 |
LOC_Os02g35010.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35000.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.763; most accessible tissue: Minghui63 flag leaf, score: 89.718 |
| vg0221002183 (J) | chr02 | 21002183 | T | TA | 66.10% | 0.00% | TA -> T | NA |
LOC_Os02g35010.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35000.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.617; most accessible tissue: Callus, score: 93.389 |
| vg0221002198 (J) | chr02 | 21002198 | T | C | 79.30% | 0.00% | T -> C | NA |
LOC_Os02g35010.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.861; most accessible tissue: Callus, score: 93.389 |
| vg0221002202 (J) | chr02 | 21002202 | A | C | 66.30% | 0.00% | C -> A |
mr1014 (All); LR P-value: 6.37E-69;
mr1072 (All); LR P-value: 9.62E-27; mr1075 (All); LR P-value: 5.45E-29; mr1101 (Jap_All); LMM P-value: 3.67E-07; mr1116 (All); LR P-value: 1.27E-16; mr1134 (All); LR P-value: 1.86E-80; mr1135 (All); LR P-value: 1.13E-73; mr1150 (Jap_All); LMM P-value: 5.39E-06; mr1202 (All); LR P-value: 8.20E-29; mr1242 (All); LR P-value: 2.34E-20; mr1242 (Jap_All); LMM P-value: 5.29E-06; mr1504 (All); LR P-value: 4.42E-86; mr1510 (All); LR P-value: 1.07E-06; mr1592 (All); LR P-value: 3.98E-14; mr1595 (All); LR P-value: 9.97E-10; mr1645 (All); LR P-value: 7.53E-40; mr1647 (All); LR P-value: 1.73E-32; mr1670 (All); LR P-value: 6.71E-34; mr1682 (All); LR P-value: 4.48E-35; mr1698 (All); LR P-value: 3.10E-21; mr1754 (All); LR P-value: 1.08E-20; mr1767 (All); LR P-value: 1.00E-17; mr1917 (All); LR P-value: 9.47E-26; mr1987 (All); LR P-value: 5.18E-102; mr1098_2 (Jap_All); LMM P-value: 6.32E-06; LR P-value: 5.84E-06; mr1114_2 (All); LR P-value: 7.96E-17; mr1128_2 (All); LR P-value: 1.82E-13; mr1148_2 (All); LR P-value: 4.80E-16; mr1150_2 (All); LR P-value: 9.40E-32; mr1198_2 (All); LR P-value: 1.42E-08; mr1205_2 (All); LR P-value: 2.37E-07; mr1239_2 (All); LR P-value: 4.12E-19; mr1242_2 (All); LR P-value: 9.25E-25; mr1258_2 (All); LR P-value: 6.04E-12; mr1275_2 (All); LR P-value: 4.09E-07; mr1496_2 (All); LR P-value: 4.02E-13; mr1657_2 (All); LR P-value: 4.20E-19; mr1670_2 (All); LR P-value: 1.19E-47; mr1698_2 (All); LR P-value: 2.10E-21; mr1936_2 (All); LR P-value: 3.12E-14; mr1944_2 (All); LR P-value: 2.33E-41 |
LOC_Os02g35010.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.778; most accessible tissue: Callus, score: 93.389 |
| vg0221002211 (J) | chr02 | 21002211 | CA | C | 66.40% | 0.00% | C -> CA | NA |
The average chromatin accessibility score: 84.639; most accessible tissue: Callus, score: 93.389
|
| vg0221002215 (J) | chr02 | 21002215 | G | C | 66.40% | 0.00% | C -> G |
mr1014 (All); LR P-value: 6.53E-69;
mr1075 (All); LR P-value: 1.01E-28; mr1116 (All); LR P-value: 1.87E-16; mr1134 (All); LR P-value: 9.80E-82; mr1135 (All); LR P-value: 3.85E-75; mr1162 (All); LR P-value: 3.94E-07; mr1242 (All); LR P-value: 6.44E-20; mr1504 (All); LR P-value: 3.26E-88; mr1510 (All); LR P-value: 9.53E-07; mr1563 (All); LR P-value: 7.01E-44; mr1595 (All); LR P-value: 1.56E-09; mr1645 (All); LR P-value: 1.29E-39; mr1647 (All); LR P-value: 3.37E-32; mr1670 (All); LR P-value: 1.99E-35; mr1672 (All); LR P-value: 1.16E-83; mr1682 (All); LR P-value: 3.13E-35; mr1714 (All); LR P-value: 5.64E-10; mr1717 (Jap_All); LMM P-value: 8.55E-07; LR P-value: 8.55E-07; mr1754 (All); LR P-value: 1.39E-20; mr1754 (Jap_All); LMM P-value: 1.37E-06; mr1917 (All); LR P-value: 8.68E-26; mr1987 (All); LR P-value: 8.78E-104; mr1114_2 (All); LR P-value: 7.73E-17; mr1128_2 (All); LR P-value: 1.80E-13; mr1148_2 (All); LR P-value: 7.13E-16; mr1150_2 (All); LR P-value: 1.34E-31; mr1205_2 (All); LR P-value: 1.09E-07; mr1217_2 (All); LR P-value: 9.92E-13; mr1239_2 (All); LR P-value: 3.16E-19; mr1242_2 (All); LR P-value: 1.17E-24; mr1258_2 (All); LR P-value: 5.11E-12; mr1275_2 (All); LR P-value: 2.37E-07; mr1496_2 (All); LR P-value: 6.19E-13; mr1575_2 (All); LR P-value: 1.10E-13; mr1670_2 (All); LR P-value: 9.79E-49; mr1698_2 (All); LR P-value: 7.14E-22; mr1767_2 (All); LR P-value: 2.22E-15; mr1873_2 (All); LR P-value: 2.02E-32; mr1944_2 (All); LR P-value: 2.29E-41 |
LOC_Os02g35010.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.520; most accessible tissue: Callus, score: 93.389 |
| vg0221002223 (J) | chr02 | 21002223 | C | A | 99.40% | 0.00% | C -> A | NA |
LOC_Os02g35010.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 84.569; most accessible tissue: Callus, score: 93.389 |
| vg0221002298 (J) | chr02 | 21002298 | T | G | 97.00% | 0.00% | T -> G | NA |
LOC_Os02g35010.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.206; most accessible tissue: Callus, score: 93.389 |
| vg0221002320 (J) | chr02 | 21002320 | T | TA | 66.40% | 0.00% | TA -> T | NA |
LOC_Os02g35010.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 86.826; most accessible tissue: Callus, score: 93.389 |
| vg0221002341 (J) | chr02 | 21002341 | A | T | 66.40% | 0.00% | T -> A |
mr1014 (All); LR P-value: 6.07E-70;
mr1075 (All); LR P-value: 2.05E-28; mr1101 (Jap_All); LMM P-value: 3.67E-07; mr1116 (All); LR P-value: 5.58E-17; mr1134 (All); LR P-value: 4.41E-82; mr1135 (All); LR P-value: 1.58E-75; mr1150 (Jap_All); LMM P-value: 5.39E-06; mr1242 (All); LR P-value: 1.88E-20; mr1242 (Jap_All); LMM P-value: 5.29E-06; mr1383 (All); LR P-value: 1.57E-23; mr1504 (All); LR P-value: 1.41E-88; mr1510 (All); LR P-value: 1.66E-06; mr1559 (All); LR P-value: 2.78E-07; mr1592 (All); LR P-value: 1.20E-13; mr1595 (All); LR P-value: 1.47E-09; mr1645 (All); LR P-value: 3.87E-40; mr1647 (All); LR P-value: 3.61E-33; mr1670 (All); LR P-value: 1.84E-34; mr1672 (All); LR P-value: 1.25E-82; mr1682 (All); LR P-value: 3.75E-37; mr1698 (All); LR P-value: 3.67E-21; mr1754 (All); LR P-value: 8.22E-22; mr1767 (All); LR P-value: 1.10E-18; mr1917 (All); LR P-value: 4.52E-26; mr1987 (All); LR P-value: 4.82E-103; mr1098_2 (Jap_All); LMM P-value: 6.32E-06; LR P-value: 5.84E-06; mr1114_2 (All); LR P-value: 1.59E-16; mr1128_2 (All); LR P-value: 2.93E-13; mr1148_2 (All); LR P-value: 7.82E-16; mr1150_2 (All); LR P-value: 8.22E-32; mr1239_2 (All); LR P-value: 1.14E-18; mr1242_2 (All); LR P-value: 1.03E-24; mr1275_2 (All); LR P-value: 1.18E-06; mr1496_2 (All); LR P-value: 5.10E-13; mr1657_2 (All); LR P-value: 9.05E-19; mr1670_2 (All); LR P-value: 2.22E-47; mr1698_2 (All); LR P-value: 3.14E-21; mr1944_2 (All); LR P-value: 6.56E-41 |
LOC_Os02g35010.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 87.839; most accessible tissue: Minghui63 flag leaf, score: 93.996 |
| vg0221002359 (J) | chr02 | 21002359 | C | CATAT | 63.70% | 0.00% | CATAT -> C | NA |
LOC_Os02g35010.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 88.065; most accessible tissue: Minghui63 flag leaf, score: 93.673 |
| vg0221002378 (J) | chr02 | 21002378 | ATCTT | A | 98.10% | 0.00% | ATCTT -> A | NA |
LOC_Os02g35010.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 88.248; most accessible tissue: Minghui63 flag leaf, score: 93.714 |
| vg0221002420 (J) | chr02 | 21002420 | GCAGAT | G | 65.50% | 0.00% | G -> GCAGAT | NA |
The average chromatin accessibility score: 88.889; most accessible tissue: Minghui63 flag leaf, score: 94.221
|
| vg0221002482 (J) | chr02 | 21002482 | A | G | 65.60% | 0.00% | G -> A |
mr1014 (All); LR P-value: 1.70E-69;
mr1075 (All); LR P-value: 2.37E-28; mr1101 (Jap_All); LMM P-value: 3.52E-07; mr1116 (All); LR P-value: 8.65E-17; mr1134 (All); LR P-value: 1.95E-81; mr1135 (All); LR P-value: 6.45E-75; mr1150 (Jap_All); LMM P-value: 5.54E-06; mr1168 (All); LR P-value: 2.75E-21; mr1242 (All); LR P-value: 2.90E-20; mr1242 (Jap_All); LMM P-value: 5.51E-06; mr1383 (All); LR P-value: 5.48E-24; mr1504 (All); LR P-value: 7.01E-88; mr1510 (All); LR P-value: 9.69E-07; mr1595 (All); LR P-value: 1.01E-09; mr1645 (All); LR P-value: 7.06E-40; mr1647 (All); LR P-value: 5.69E-33; mr1670 (All); LR P-value: 5.21E-34; mr1672 (All); LR P-value: 1.09E-81; mr1682 (All); LR P-value: 2.64E-37; mr1698 (All); LR P-value: 7.86E-22; mr1754 (All); LR P-value: 9.02E-22; mr1767 (All); LR P-value: 1.15E-18; mr1917 (All); LR P-value: 6.81E-26; mr1987 (All); LR P-value: 5.30E-102; mr1098_2 (Jap_All); LMM P-value: 7.07E-06; LR P-value: 6.39E-06; mr1128_2 (All); LR P-value: 9.60E-13; mr1148_2 (All); LR P-value: 1.48E-15; mr1150_2 (All); LR P-value: 2.40E-31; mr1239_2 (All); LR P-value: 3.29E-18; mr1242_2 (All); LR P-value: 2.77E-24; mr1657_2 (All); LR P-value: 1.82E-18; mr1670_2 (All); LR P-value: 1.04E-46; mr1698_2 (All); LR P-value: 9.43E-22 |
LOC_Os02g35010.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 90.055; most accessible tissue: Minghui63 flag leaf, score: 93.996 |
| vg0221002490 (J) | chr02 | 21002490 | GCCTAGA GC | G | 66.20% | 0.00% | G -> GCCTAGAGC | NA |
The average chromatin accessibility score: 90.206; most accessible tissue: Minghui63 flag leaf, score: 94.184
|
| vg0221002553 (J) | chr02 | 21002553 | G | C | 99.80% | 0.00% | G -> C | NA |
LOC_Os02g35010.1 Alt: C| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 90.891; most accessible tissue: Minghui63 flower, score: 93.866 |
| vg0221002577 (J) | chr02 | 21002577 | C | T | 59.40% | 0.36% | C -> T |
LOC_Os02g35010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g35010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 89.845; most accessible tissue: Minghui63 flag leaf, score: 94.221 |
|
| vg0221002595 (J) | chr02 | 21002595 | T | G | 66.40% | 0.00% | G -> T |
mr1014 (All); LR P-value: 6.07E-70;
mr1075 (All); LR P-value: 2.05E-28; mr1101 (Jap_All); LMM P-value: 3.67E-07; mr1116 (All); LR P-value: 5.58E-17; mr1134 (All); LR P-value: 4.41E-82; mr1135 (All); LR P-value: 1.58E-75; mr1150 (Jap_All); LMM P-value: 5.39E-06; mr1242 (All); LR P-value: 1.88E-20; mr1242 (Jap_All); LMM P-value: 5.29E-06; mr1383 (All); LR P-value: 1.57E-23; mr1504 (All); LR P-value: 1.41E-88; mr1510 (All); LR P-value: 1.66E-06; mr1559 (All); LR P-value: 2.78E-07; mr1592 (All); LR P-value: 1.20E-13; mr1595 (All); LR P-value: 1.47E-09; mr1645 (All); LR P-value: 3.87E-40; mr1647 (All); LR P-value: 3.61E-33; mr1670 (All); LR P-value: 1.84E-34; mr1672 (All); LR P-value: 1.25E-82; mr1682 (All); LR P-value: 3.75E-37; mr1698 (All); LR P-value: 3.67E-21; mr1754 (All); LR P-value: 8.22E-22; mr1767 (All); LR P-value: 1.10E-18; mr1917 (All); LR P-value: 4.52E-26; mr1987 (All); LR P-value: 4.82E-103; mr1098_2 (Jap_All); LMM P-value: 6.32E-06; LR P-value: 5.84E-06; mr1114_2 (All); LR P-value: 1.59E-16; mr1128_2 (All); LR P-value: 2.93E-13; mr1148_2 (All); LR P-value: 7.82E-16; mr1150_2 (All); LR P-value: 8.22E-32; mr1239_2 (All); LR P-value: 1.14E-18; mr1242_2 (All); LR P-value: 1.03E-24; mr1275_2 (All); LR P-value: 1.18E-06; mr1496_2 (All); LR P-value: 5.10E-13; mr1657_2 (All); LR P-value: 9.05E-19; mr1670_2 (All); LR P-value: 2.22E-47; mr1698_2 (All); LR P-value: 3.14E-21; mr1944_2 (All); LR P-value: 6.56E-41 |
LOC_Os02g35010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.867; most accessible tissue: Minghui63 flag leaf, score: 94.073 |
| vg0221002708 (J) | chr02 | 21002708 | C | T | 97.00% | 0.00% | C -> T | NA |
LOC_Os02g35010.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.413; most accessible tissue: Minghui63 flag leaf, score: 94.329 |
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