9 variations found. Os11g0121500/LOC_Os11g02840 (protein kinase; putative; expressed), ranging from 959,795 bp to 961,058 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os11g02840 | protein kinase, putative; RAP ID: Os11g0121500; MSU ID: LOC_Os11g02840 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1100959843 (J) | chr11 | 959843 | G | A | 95.80% | 1.95% | G -> A | NA |
LOC_Os11g02840.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g02840.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 85.568; most accessible tissue: Zhenshan97 flower, score: 95.876 |
| vg1100959851 (J) | chr11 | 959851 | C | CT | 95.50% | 0.00% | C -> CT | NA |
The average chromatin accessibility score: 85.732; most accessible tissue: Zhenshan97 flower, score: 95.855
|
| vg1100959953 (J) | chr11 | 959953 | C | A | 60.00% | 0.00% | A -> C |
mr1016 (Ind_All); LR P-value: 2.53E-17;
mr1017 (Ind_All); LR P-value: 8.57E-14; mr1022 (Ind_All); LR P-value: 1.63E-16; mr1023 (Ind_All); LR P-value: 2.76E-12; mr1055 (Ind_All); LR P-value: 4.74E-18; mr1079 (Ind_All); LR P-value: 8.03E-17; mr1082 (Ind_All); LR P-value: 4.71E-07; mr1085 (All); LR P-value: 3.61E-31; mr1089 (All); LR P-value: 1.46E-42; mr1093 (All); LR P-value: 6.25E-43; mr1093 (Ind_All); LR P-value: 1.13E-08; mr1107 (All); LR P-value: 1.72E-29; mr1109 (All); LR P-value: 1.88E-49; mr1129 (All); LR P-value: 3.06E-34; mr1132 (Ind_All); LR P-value: 1.04E-15; mr1142 (Ind_All); LR P-value: 3.39E-15; mr1145 (All); LR P-value: 5.20E-27; mr1178 (Ind_All); LR P-value: 3.89E-15; mr1195 (All); LR P-value: 4.78E-10; mr1226 (All); LR P-value: 1.91E-32; mr1226 (Ind_All); LR P-value: 3.52E-07; mr1235 (All); LR P-value: 7.82E-39; mr1235 (Ind_All); LR P-value: 6.26E-06; mr1243 (All); LR P-value: 6.76E-35; mr1251 (All); LR P-value: 2.97E-26; mr1257 (All); LR P-value: 8.03E-31; mr1264 (All); LR P-value: 7.43E-24; mr1299 (All); LR P-value: 1.51E-09; mr1301 (Ind_All); LR P-value: 6.98E-11; mr1390 (Ind_All); LR P-value: 1.79E-16; mr1410 (Ind_All); LR P-value: 5.36E-09; mr1411 (All); LR P-value: 1.03E-29; mr1411 (Ind_All); LR P-value: 3.49E-08; mr1425 (Ind_All); LR P-value: 6.12E-07; mr1435 (All); LR P-value: 2.61E-38; mr1489 (Ind_All); LR P-value: 5.38E-08; mr1490 (Ind_All); LR P-value: 7.83E-16; mr1491 (Ind_All); LR P-value: 2.94E-14; mr1541 (All); LR P-value: 1.77E-20; mr1546 (Ind_All); LR P-value: 1.58E-11; mr1599 (All); LR P-value: 4.54E-56; mr1599 (Ind_All); LR P-value: 3.88E-07; mr1737 (All); LR P-value: 2.46E-29; mr1805 (Ind_All); LR P-value: 2.45E-07; mr1905 (All); LR P-value: 5.58E-10; mr1938 (All); LR P-value: 2.57E-11; mr1982 (All); LR P-value: 2.34E-13; mr1022_2 (Ind_All); LR P-value: 3.13E-18; mr1023_2 (Ind_All); LR P-value: 2.21E-14; mr1055_2 (Ind_All); LR P-value: 6.83E-19; mr1064_2 (Ind_All); LR P-value: 3.96E-06; mr1079_2 (Ind_All); LR P-value: 1.01E-17; mr1089_2 (All); LR P-value: 2.42E-51; mr1093_2 (Ind_All); LR P-value: 2.20E-08; mr1109_2 (All); LR P-value: 1.72E-56; mr1129_2 (All); LR P-value: 1.75E-37; mr1132_2 (Ind_All); LR P-value: 4.06E-18; mr1178_2 (Ind_All); LR P-value: 1.30E-19; mr1226_2 (All); LR P-value: 1.29E-41; mr1235_2 (Ind_All); LR P-value: 4.64E-08; mr1243_2 (All); LR P-value: 3.98E-43; mr1251_2 (All); LR P-value: 3.27E-39; mr1255_2 (All); LR P-value: 1.45E-20; mr1257_2 (All); LR P-value: 5.17E-36; mr1377_2 (All); LR P-value: 2.13E-11; mr1390_2 (Ind_All); LR P-value: 1.00E-19; mr1435_2 (All); LR P-value: 1.87E-39; mr1489_2 (Ind_All); LR P-value: 3.13E-11; mr1490_2 (Ind_All); LR P-value: 3.76E-18; mr1551_2 (All); LR P-value: 2.24E-22; mr1578_2 (All); LR P-value: 2.06E-16; mr1599_2 (All); LR P-value: 9.76E-62; mr1819_2 (All); LR P-value: 4.92E-07; mr1938_2 (All); LR P-value: 4.07E-15 |
LOC_Os11g02840.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 85.868; most accessible tissue: Zhenshan97 flower, score: 95.247 |
| vg1100960099 (J) | chr11 | 960099 | C | A | 95.50% | 0.00% | C -> A,T | NA |
LOC_Os11g02840.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os11g02850.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g02840.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 77.078; most accessible tissue: Zhenshan97 flower, score: 92.513 |
| vg1100960267 (J) | chr11 | 960267 | TA | T | 60.20% | 0.00% | T -> TA | NA |
LOC_Os11g02850.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g02840.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.255; most accessible tissue: Zhenshan97 flower, score: 88.571 |
| vg1100960277 (J) | chr11 | 960277 | GT | GTT | 64.50% | 0.00% | GTT -> GT,G,GTTT | NA |
LOC_Os11g02850.1 Alt: GTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g02840.1 Alt: GTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02850.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02840.1 Alt: GT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02850.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g02840.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.546; most accessible tissue: Zhenshan97 flower, score: 88.727 |
| vg1100960488 (J) | chr11 | 960488 | G | T | 80.30% | 0.00% | T -> G | NA |
LOC_Os11g02850.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g02840.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.676; most accessible tissue: Zhenshan97 flower, score: 92.866 |
| vg1100960795 (J) | chr11 | 960795 | T | C | 59.90% | 0.00% | C -> T |
mr1016 (Ind_All); LR P-value: 1.04E-15;
mr1017 (Ind_All); LR P-value: 7.24E-13; mr1022 (Ind_All); LR P-value: 7.78E-15; mr1023 (Ind_All); LR P-value: 4.13E-11; mr1055 (Ind_All); LR P-value: 8.73E-17; mr1079 (Ind_All); LR P-value: 8.58E-15; mr1082 (All); LR P-value: 9.22E-39; mr1082 (Ind_All); LR P-value: 4.97E-07; mr1085 (All); LR P-value: 2.58E-29; mr1093 (All); LR P-value: 2.39E-41; mr1093 (Ind_All); LR P-value: 1.73E-08; mr1103 (All); LR P-value: 2.12E-55; mr1109 (All); LR P-value: 6.54E-47; mr1132 (Ind_All); LR P-value: 4.26E-14; mr1142 (Ind_All); LR P-value: 2.19E-13; mr1178 (Ind_All); LR P-value: 1.78E-13; mr1204 (All); LR P-value: 9.94E-30; mr1226 (All); LR P-value: 6.19E-33; mr1243 (All); LR P-value: 2.16E-33; mr1251 (All); LR P-value: 3.57E-25; mr1257 (All); LR P-value: 5.23E-30; mr1264 (All); LR P-value: 5.81E-24; mr1299 (All); LR P-value: 2.17E-09; mr1301 (Ind_All); LR P-value: 1.76E-10; mr1390 (Ind_All); LR P-value: 2.18E-14; mr1410 (Ind_All); LR P-value: 2.46E-08; mr1411 (All); LR P-value: 2.39E-29; mr1411 (Ind_All); LR P-value: 3.18E-07; mr1435 (All); LR P-value: 1.11E-36; mr1437 (All); LR P-value: 8.18E-40; mr1489 (Ind_All); LR P-value: 1.30E-07; mr1490 (Ind_All); LR P-value: 6.70E-14; mr1491 (Ind_All); LR P-value: 9.96E-13; mr1541 (All); LR P-value: 7.46E-20; mr1546 (Ind_All); LR P-value: 1.37E-09; mr1599 (All); LR P-value: 3.83E-54; mr1805 (Ind_All); LR P-value: 7.02E-07; mr1905 (All); LR P-value: 1.30E-09; mr1022_2 (Ind_All); LR P-value: 1.49E-15; mr1023_2 (Ind_All); LR P-value: 9.01E-13; mr1055_2 (Ind_All); LR P-value: 2.62E-16; mr1079_2 (Ind_All); LR P-value: 2.47E-15; mr1132_2 (Ind_All); LR P-value: 2.99E-16; mr1178_2 (Ind_All); LR P-value: 2.12E-17; mr1226_2 (All); LR P-value: 1.65E-41; mr1255_2 (All); LR P-value: 1.46E-19; mr1390_2 (Ind_All); LR P-value: 5.20E-17; mr1489_2 (Ind_All); LR P-value: 4.31E-10; mr1490_2 (Ind_All); LR P-value: 1.24E-15; mr1551_2 (All); LR P-value: 2.64E-22; mr1578_2 (All); LR P-value: 6.85E-15; mr1938_2 (All); LR P-value: 7.60E-15 |
LOC_Os11g02850.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g02840.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.824; most accessible tissue: Zhenshan97 panicle, score: 97.834 |
| vg1100960864 (J) | chr11 | 960864 | G | A | 65.20% | 0.00% | A -> G |
mr1016 (All); LR P-value: 3.44E-46;
mr1016 (Ind_All); LR P-value: 5.76E-20; mr1017 (Ind_All); LR P-value: 4.97E-16; mr1018 (Ind_All); LR P-value: 2.24E-07; mr1022 (All); LR P-value: 9.38E-28; mr1022 (Ind_All); LR P-value: 1.15E-17; mr1023 (Ind_All); LR P-value: 4.81E-16; mr1055 (Ind_All); LR P-value: 1.22E-20; mr1079 (Ind_All); LR P-value: 3.82E-20; mr1082 (All); LR P-value: 4.44E-41; mr1082 (Ind_All); LR P-value: 1.74E-07; mr1089 (Ind_All); LR P-value: 1.07E-06; mr1093 (Ind_All); LR P-value: 9.80E-11; mr1103 (Ind_All); LR P-value: 6.54E-06; mr1107 (All); LR P-value: 3.51E-30; mr1132 (All); LR P-value: 1.82E-69; mr1132 (Ind_All); LMM P-value: 1.77E-06; LR P-value: 1.42E-19; mr1141 (All); LR P-value: 5.12E-43; mr1142 (Ind_All); LR P-value: 6.44E-19; mr1178 (Ind_All); LR P-value: 4.61E-17; mr1226 (All); LR P-value: 2.50E-28; mr1226 (Ind_All); LR P-value: 3.13E-07; mr1235 (Ind_All); LR P-value: 1.78E-07; mr1243 (All); LR P-value: 6.10E-31; mr1301 (Ind_All); LR P-value: 2.95E-11; mr1390 (All); LR P-value: 2.85E-54; mr1390 (Ind_All); LR P-value: 2.71E-19; mr1410 (Ind_All); LR P-value: 1.14E-07; mr1411 (All); LR P-value: 1.09E-25; mr1411 (Ind_All); LR P-value: 1.89E-08; mr1425 (Ind_All); LR P-value: 3.40E-06; mr1489 (Ind_All); LR P-value: 3.03E-12; mr1490 (All); LR P-value: 2.78E-53; mr1490 (Ind_All); LR P-value: 4.34E-18; mr1491 (Ind_All); LMM P-value: 6.26E-06; LR P-value: 6.35E-18; mr1495 (All); LR P-value: 1.15E-22; mr1546 (All); LR P-value: 1.44E-29; mr1546 (Ind_All); LR P-value: 1.82E-12; mr1560 (Ind_All); LR P-value: 6.58E-06; mr1599 (All); LR P-value: 1.17E-50; mr1599 (Ind_All); LR P-value: 4.06E-09; mr1645 (All); LR P-value: 4.89E-39; mr1719 (All); LR P-value: 3.31E-37; mr1733 (All); LR P-value: 4.71E-33; mr1767 (All); LR P-value: 8.80E-18; mr1805 (Ind_All); LR P-value: 2.09E-09; mr1905 (All); LR P-value: 1.42E-10; mr1022_2 (Ind_All); LR P-value: 1.71E-17; mr1023_2 (Ind_All); LR P-value: 1.09E-13; mr1055_2 (Ind_All); LR P-value: 5.38E-19; mr1079_2 (Ind_All); LR P-value: 3.44E-17; mr1089_2 (Ind_All); LR P-value: 1.60E-08; mr1093_2 (Ind_All); LR P-value: 1.24E-10; mr1132_2 (Ind_All); LR P-value: 1.12E-17; mr1178_2 (Ind_All); LR P-value: 2.03E-18; mr1235_2 (All); LR P-value: 7.14E-52; mr1235_2 (Ind_All); LR P-value: 7.92E-10; mr1243_2 (All); LR P-value: 1.03E-42; mr1243_2 (Ind_All); LR P-value: 2.25E-07; mr1390_2 (Ind_All); LR P-value: 5.60E-19; mr1403_2 (All); LR P-value: 2.48E-24; mr1403_2 (Ind_All); LR P-value: 2.03E-06; mr1416_2 (All); LR P-value: 2.05E-17; mr1489_2 (Ind_All); LR P-value: 3.89E-11; mr1490_2 (Ind_All); LR P-value: 1.13E-17; mr1546_2 (All); LR P-value: 5.68E-46; mr1587_2 (Ind_All); LR P-value: 7.51E-06; mr1599_2 (All); LR P-value: 4.76E-59; mr1599_2 (Ind_All); LR P-value: 2.27E-09; mr1805_2 (Ind_All); LR P-value: 6.55E-09; mr1993_2 (Ind_All); LR P-value: 9.26E-08 |
LOC_Os11g02840.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.910; most accessible tissue: Zhenshan97 panicle, score: 97.974 |