32 variations found. Os08g0506400/LOC_Os08g39590 (inactive receptor kinase At2g26730 precursor; putative; expressed), ranging from 25,060,739 bp to 25,063,403 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os08g39590 | inactive receptor kinase At2g26730 precursor, putative, expressed; RAP ID: Os08g0506400; MSU ID: LOC_Os08g39590 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0825060808 (J) | chr08 | 25060808 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os08g39590.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g39600.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 98.818; most accessible tissue: Callus, score: 99.777 |
| vg0825060858 (J) | chr08 | 25060858 | C | CGGCGGT | 99.90% | 0.00% | C -> CGGCGGT | NA |
LOC_Os08g39590.1 Alt: CGGCGGT| disruptive_inframe_insertion MODERATE(snpEff)
LOC_Os08g39600.1 Alt: CGGCGGT| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.924; most accessible tissue: Zhenshan97 panicle, score: 99.437 |
| vg0825060867 (J) | chr08 | 25060867 | CGGTGGT GGT | CGGT | 99.40% | 0.00% | CGGTGGTGGT -> CGGT,C,CGG TGGTGGTGGT | NA |
LOC_Os08g39590.1 Alt: CGGT| inframe_deletion MODERATE(snpEff)
LOC_Os08g39600.1 Alt: CGGT| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39590.1 Alt: C| inframe_deletion MODERATE(snpEff) LOC_Os08g39600.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39590.1 Alt: CGGTGGTGGTGGT| inframe_insertion MODERATE(snpEff) LOC_Os08g39600.1 Alt: CGGTGGTGGTGGT| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.687; most accessible tissue: Zhenshan97 panicle, score: 99.346 |
| vg0825060873 (J) | chr08 | 25060873 | T | C | 70.70% | 0.00% | T -> C,TGGC |
mr1699 (Ind_All); LR P-value: 1.43E-06;
mr1874 (All); LMM P-value: 2.61E-17; LR P-value: 3.51E-41; mr1874 (Ind_All); LMM P-value: 7.09E-17; LR P-value: 9.77E-24; mr1699_2 (All); LMM P-value: 5.95E-06; mr1699_2 (Ind_All); LMM P-value: 8.73E-07; LR P-value: 1.32E-09; mr1874_2 (All); LMM P-value: 2.56E-21; LR P-value: 3.24E-62; mr1874_2 (Ind_All); LMM P-value: 3.38E-20; LR P-value: 8.21E-33 |
LOC_Os08g39590.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g39590.1 Alt: TGGC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 96.642; most accessible tissue: Zhenshan97 panicle, score: 99.339 |
| vg0825060904 (J) | chr08 | 25060904 | G | T | 69.00% | 0.00% | G -> T |
mr1699 (Ind_All); LR P-value: 1.43E-06;
mr1874 (All); LMM P-value: 2.61E-17; LR P-value: 3.51E-41; mr1874 (Ind_All); LMM P-value: 7.09E-17; LR P-value: 9.77E-24; mr1699_2 (All); LMM P-value: 5.95E-06; mr1699_2 (Ind_All); LMM P-value: 8.73E-07; LR P-value: 1.32E-09; mr1874_2 (All); LMM P-value: 2.56E-21; LR P-value: 3.24E-62; mr1874_2 (Ind_All); LMM P-value: 3.38E-20; LR P-value: 8.21E-33 |
LOC_Os08g39590.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 96.573; most accessible tissue: Zhenshan97 panicle, score: 99.307 |
| vg0825060910 (J) | chr08 | 25060910 | T | G | 99.90% | 0.00% | T -> G | NA |
LOC_Os08g39590.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os08g39600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.613; most accessible tissue: Zhenshan97 panicle, score: 99.314 |
| vg0825061024 (J) | chr08 | 25061024 | G | A | 99.20% | 0.00% | G -> A | NA |
LOC_Os08g39590.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.808; most accessible tissue: Zhenshan97 panicle, score: 97.252 |
| vg0825061090 (J) | chr08 | 25061090 | C | T | 95.30% | 0.00% | C -> T | NA |
LOC_Os08g39590.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.253; most accessible tissue: Zhenshan97 panicle, score: 97.174 |
| vg0825061237 (J) | chr08 | 25061237 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os08g39590.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os08g39600.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.405; most accessible tissue: Zhenshan97 panicle, score: 94.880 |
| vg0825061246 (J) | chr08 | 25061246 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os08g39590.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os08g39600.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.400; most accessible tissue: Zhenshan97 panicle, score: 94.880 |
| vg0825061252 (J) | chr08 | 25061252 | G | T | 69.10% | 0.00% | G -> T |
mr1699 (Ind_All); LR P-value: 2.03E-06;
mr1874 (All); LMM P-value: 6.25E-19; LR P-value: 4.13E-43; mr1874 (Ind_All); LMM P-value: 4.00E-17; LR P-value: 3.12E-24; mr1699_2 (All); LMM P-value: 5.75E-07; mr1699_2 (Ind_All); LMM P-value: 8.71E-07; LR P-value: 9.88E-10; mr1874_2 (All); LMM P-value: 2.95E-22; LR P-value: 1.34E-63; mr1874_2 (Ind_All); LMM P-value: 4.62E-21; LR P-value: 9.51E-34 |
LOC_Os08g39590.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.537; most accessible tissue: Zhenshan97 panicle, score: 94.880 |
| vg0825061351 (J) | chr08 | 25061351 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os08g39590.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os08g39600.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.863; most accessible tissue: Zhenshan97 panicle, score: 94.518 |
| vg0825061847 (J) | chr08 | 25061847 | T | C | 99.20% | 0.00% | T -> C | NA |
LOC_Os08g39590.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 84.331; most accessible tissue: Zhenshan97 panicle, score: 94.880 |
| vg0825062039 (J) | chr08 | 25062039 | C | G | 95.90% | 0.80% | C -> G | NA |
LOC_Os08g39590.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g39590.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 88.937; most accessible tissue: Zhenshan97 panicle, score: 95.951 |
| vg0825062188 (J) | chr08 | 25062188 | G | C | 30.50% | 9.27% | C -> G | NA |
LOC_Os08g39590.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os08g39600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 90.950; most accessible tissue: Zhenshan97 panicle, score: 96.294 |
| vg0825062483 (J) | chr08 | 25062483 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os08g39590.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.168; most accessible tissue: Zhenshan97 panicle, score: 97.490 |
| vg0825062583 (J) | chr08 | 25062583 | C | T | 73.80% | 4.76% | C -> T | NA |
LOC_Os08g39590.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g39590.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.778; most accessible tissue: Zhenshan97 panicle, score: 97.702 |
| vg0825062895 (J) | chr08 | 25062895 | C | G | 89.50% | 0.00% | C -> G | NA |
LOC_Os08g39590.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g39610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.481; most accessible tissue: Zhenshan97 panicle, score: 98.779 |
| vg0825062896 (J) | chr08 | 25062896 | G | A | 89.50% | 0.00% | G -> A | NA |
LOC_Os08g39590.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39600.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g39610.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.463; most accessible tissue: Zhenshan97 panicle, score: 98.771 |
| vg0825062898 (J) | chr08 | 25062898 | C | T | 80.40% | 0.00% | C -> T |
LOC_Os08g39590.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39600.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g39610.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.587; most accessible tissue: Zhenshan97 panicle, score: 98.827 |
|
| vg0825062905 (J) | chr08 | 25062905 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os08g39590.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g39600.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39610.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 88.823; most accessible tissue: Zhenshan97 panicle, score: 98.955 |
| vg0825062931 (J) | chr08 | 25062931 | ACTACTC | A | 79.70% | 3.62% | ACTACTC -> A | NA |
LOC_Os08g39590.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39600.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g39610.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 91.227; most accessible tissue: Zhenshan97 panicle, score: 99.005 |
| vg0825062934 (J) | chr08 | 25062934 | ACTC | A | 69.00% | 0.17% | ACTC -> A | NA |
LOC_Os08g39590.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39600.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g39610.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 91.217; most accessible tissue: Zhenshan97 panicle, score: 99.005 |
| vg0825062950 (J) | chr08 | 25062950 | G | GC | 99.90% | 0.00% | G -> GC | NA |
LOC_Os08g39590.1 Alt: GC| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g39600.1 Alt: GC| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39610.1 Alt: GC| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.681; most accessible tissue: Zhenshan97 panicle, score: 99.024 |
| vg0825062988 (J) | chr08 | 25062988 | A | G | 99.60% | 0.00% | A -> G | NA |
LOC_Os08g39590.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g39610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 90.046; most accessible tissue: Zhenshan97 panicle, score: 99.036 |
| vg0825063218 (J) | chr08 | 25063218 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os08g39590.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g39600.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39610.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.949; most accessible tissue: Zhenshan97 panicle, score: 98.612 |
| vg0825063261 (J) | chr08 | 25063261 | GAA | GAAA | 99.80% | 0.00% | GAA -> GAAA,G,GA | NA |
LOC_Os08g39590.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g39600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39590.1 Alt: GA| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os08g39600.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39610.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39590.1 Alt: GAAA| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os08g39600.1 Alt: GAAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39610.1 Alt: GAAA| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 88.949; most accessible tissue: Zhenshan97 panicle, score: 98.658 |
| vg0825063292 (J) | chr08 | 25063292 | C | G | 99.80% | 0.00% | C -> G | NA |
LOC_Os08g39590.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g39600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g39610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.596; most accessible tissue: Zhenshan97 panicle, score: 98.811 |
| vg0825063353 (J) | chr08 | 25063353 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os08g39590.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g39600.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39610.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.973; most accessible tissue: Zhenshan97 panicle, score: 98.324 |
| vg0825063378 (J) | chr08 | 25063378 | GA | G | 99.90% | 0.00% | GA -> G | NA |
LOC_Os08g39590.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g39600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.873; most accessible tissue: Zhenshan97 panicle, score: 98.272 |
| vg0825063380 (J) | chr08 | 25063380 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os08g39590.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g39600.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39610.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.894; most accessible tissue: Zhenshan97 panicle, score: 98.272 |
| vg0825063383 (J) | chr08 | 25063383 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os08g39590.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g39600.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g39610.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.644; most accessible tissue: Zhenshan97 panicle, score: 98.258 |