10 variations found. Os02g0647300/LOC_Os02g43250 (receptor-like protein kinase precursor; putative; expressed), ranging from 26,052,819 bp to 26,054,216 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g43250 | receptor-like protein kinase precursor, putative, expressed; RAP ID: Os02g0647300; MSU ID: LOC_Os02g43250 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0226052907 (J) | chr02 | 26052907 | T | G | 69.70% | 0.00% | G -> T |
LOC_Os02g43250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 98.483; most accessible tissue: Zhenshan97 panicle, score: 99.663 |
|
| vg0226052991 (J) | chr02 | 26052991 | C | T | 79.70% | 0.00% | C -> T |
mr1069 (Ind_All); LR P-value: 1.79E-07;
mr1072 (Ind_All); LR P-value: 7.14E-08; mr1074 (Ind_All); LR P-value: 1.22E-08; mr1075 (Ind_All); LR P-value: 3.18E-07; mr1077 (Ind_All); LR P-value: 1.59E-07; mr1080 (Ind_All); LR P-value: 9.09E-06; mr1124 (Ind_All); LR P-value: 1.28E-07; mr1130 (Ind_All); LR P-value: 6.67E-08; mr1148 (Ind_All); LR P-value: 5.09E-06; mr1150 (Ind_All); LR P-value: 4.76E-06; mr1180 (Ind_All); LR P-value: 1.10E-07; mr1193 (All); LR P-value: 7.64E-08; mr1202 (Ind_All); LR P-value: 7.45E-07; mr1441 (Ind_All); LR P-value: 6.49E-07; mr1861 (Ind_All); LR P-value: 1.28E-07; mr1918 (Ind_All); LR P-value: 1.52E-09; mr1934 (Ind_All); LR P-value: 1.49E-08; mr1935 (Ind_All); LR P-value: 3.73E-09; mr1962 (Ind_All); LR P-value: 1.39E-08; mr1072_2 (Ind_All); LR P-value: 1.22E-10; mr1074_2 (Ind_All); LR P-value: 3.24E-06; mr1075_2 (Ind_All); LR P-value: 2.16E-11; mr1077_2 (Ind_All); LR P-value: 1.49E-12; mr1098_2 (Ind_All); LR P-value: 5.80E-06; mr1124_2 (Ind_All); LR P-value: 1.92E-11; mr1149_2 (Ind_All); LR P-value: 7.05E-11; mr1150_2 (Ind_All); LR P-value: 2.52E-08; mr1174_2 (Ind_All); LR P-value: 2.32E-08; mr1222_2 (Ind_All); LR P-value: 1.35E-07; mr1332_2 (Ind_All); LR P-value: 2.41E-06; mr1347_2 (Ind_All); LR P-value: 5.00E-10; mr1441_2 (Ind_All); LR P-value: 4.16E-12; mr1558_2 (Ind_All); LR P-value: 5.47E-06; mr1592_2 (Ind_All); LR P-value: 1.40E-06; mr1598_2 (Ind_All); LR P-value: 3.11E-10; mr1619_2 (Ind_All); LR P-value: 5.44E-07; mr1861_2 (Ind_All); LR P-value: 2.63E-15; mr1895_2 (Ind_All); LR P-value: 2.77E-06; mr1918_2 (Ind_All); LR P-value: 1.73E-06; mr1928_2 (Ind_All); LR P-value: 1.24E-06; mr1931_2 (Ind_All); LR P-value: 5.14E-06; mr1962_2 (Ind_All); LR P-value: 5.06E-13 |
LOC_Os02g43250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 98.902; most accessible tissue: Zhenshan97 panicle, score: 99.739 |
| vg0226053265 (J) | chr02 | 26053265 | C | T | 98.50% | 0.00% | C -> T | NA |
LOC_Os02g43250.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 97.276; most accessible tissue: Zhenshan97 panicle, score: 99.379 |
| vg0226053379 (J) | chr02 | 26053379 | C | A | 93.40% | 0.80% | C -> A | NA |
LOC_Os02g43250.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g43250.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 92.713; most accessible tissue: Zhenshan97 panicle, score: 98.901 |
| vg0226053588 (J) | chr02 | 26053588 | C | T | 79.50% | 0.00% | C -> T |
mr1069 (Ind_All); LR P-value: 3.30E-07;
mr1072 (Ind_All); LR P-value: 1.25E-07; mr1074 (Ind_All); LR P-value: 3.41E-08; mr1075 (Ind_All); LR P-value: 4.79E-07; mr1077 (Ind_All); LR P-value: 5.33E-07; mr1124 (Ind_All); LR P-value: 1.89E-07; mr1130 (Ind_All); LR P-value: 1.44E-07; mr1180 (Ind_All); LR P-value: 1.62E-07; mr1193 (All); LR P-value: 5.35E-08; mr1202 (Ind_All); LR P-value: 1.05E-06; mr1441 (Ind_All); LR P-value: 1.40E-06; mr1861 (Ind_All); LR P-value: 2.61E-07; mr1918 (Ind_All); LR P-value: 2.99E-09; mr1934 (Ind_All); LR P-value: 6.07E-09; mr1935 (Ind_All); LR P-value: 1.27E-08; mr1962 (Ind_All); LR P-value: 5.39E-08; mr1072_2 (Ind_All); LR P-value: 2.37E-10; mr1074_2 (Ind_All); LR P-value: 3.55E-06; mr1075_2 (Ind_All); LR P-value: 5.49E-11; mr1077_2 (Ind_All); LR P-value: 1.55E-11; mr1098_2 (Ind_All); LR P-value: 6.99E-06; mr1124_2 (Ind_All); LR P-value: 3.56E-11; mr1149_2 (Ind_All); LR P-value: 1.74E-10; mr1150_2 (Ind_All); LR P-value: 4.92E-08; mr1174_2 (Ind_All); LR P-value: 9.55E-08; mr1222_2 (Ind_All); LR P-value: 1.51E-07; mr1332_2 (Ind_All); LR P-value: 7.56E-06; mr1347_2 (Ind_All); LR P-value: 1.13E-09; mr1441_2 (Ind_All); LR P-value: 1.30E-11; mr1558_2 (Ind_All); LR P-value: 8.71E-06; mr1592_2 (Ind_All); LR P-value: 3.66E-06; mr1598_2 (Ind_All); LR P-value: 1.28E-09; mr1619_2 (Ind_All); LR P-value: 6.84E-07; mr1861_2 (Ind_All); LR P-value: 1.32E-14; mr1918_2 (Ind_All); LR P-value: 3.19E-06; mr1928_2 (Ind_All); LR P-value: 1.29E-06; mr1931_2 (Ind_All); LR P-value: 8.80E-06; mr1934_2 (Ind_All); LR P-value: 3.85E-08; mr1962_2 (Ind_All); LR P-value: 1.47E-12 |
LOC_Os02g43250.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.592; most accessible tissue: Zhenshan97 panicle, score: 97.974 |
| vg0226054006 (J) | chr02 | 26054006 | C | T | 93.40% | 0.00% | C -> T | NA |
LOC_Os02g43250.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 96.188; most accessible tissue: Zhenshan97 panicle, score: 99.382 |
| vg0226054012 (J) | chr02 | 26054012 | C | A | 95.70% | 0.00% | C -> A | NA |
LOC_Os02g43250.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 96.342; most accessible tissue: Zhenshan97 panicle, score: 99.416 |
| vg0226054119 (J) | chr02 | 26054119 | CGGA | C | 98.50% | 0.00% | CGGA -> C | NA |
LOC_Os02g43250.1 Alt: C| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 97.088; most accessible tissue: Zhenshan97 panicle, score: 99.569 |
| vg0226054186 (J) | chr02 | 26054186 | A | G | 63.90% | 0.00% | G -> A | NA |
LOC_Os02g43250.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g43260.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.455; most accessible tissue: Callus, score: 99.794 |
| STR0226054185 (J) | chr02 | 26054185 | GA | GG | 59.00% | 0.00% | GG -> GA | NA |
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