132 variations found. Os01g0114700/LOC_Os01g02440 (Ser%2FThr receptor-like kinase; putative; expressed), ranging from 789,966 bp to 792,411 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g02440 | Ser/Thr receptor-like kinase, putative, expressed; RAP ID: Os01g0114700; MSU ID: LOC_Os01g02440 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0100790202 (J) | chr01 | 790202 | C | T | 33.10% | 42.64% | C -> T |
mr1059 (Ind_All); LR P-value: 5.29E-09;
mr1143 (Ind_All); LR P-value: 3.00E-11; mr1167 (Ind_All); LR P-value: 7.20E-10; mr1535 (Ind_All); LR P-value: 9.56E-10; mr1593 (Ind_All); LR P-value: 5.73E-09; mr1675 (Ind_All); LR P-value: 8.38E-10; mr1726 (Ind_All); LR P-value: 2.11E-07; mr1739 (All); LR P-value: 5.80E-08; mr1739 (Ind_All); LR P-value: 3.48E-08; mr1950 (Ind_All); LR P-value: 6.29E-07; mr1969 (Ind_All); LR P-value: 6.70E-10; mr1995 (Ind_All); LR P-value: 1.39E-11; mr1158_2 (Ind_All); LR P-value: 3.39E-06; mr1167_2 (Ind_All); LR P-value: 8.58E-09; mr1360_2 (Ind_All); LR P-value: 8.52E-06; mr1378_2 (Ind_All); LR P-value: 1.57E-06; mr1383_2 (Ind_All); LR P-value: 5.23E-08; mr1458_2 (Ind_All); LR P-value: 2.72E-07; mr1593_2 (Ind_All); LR P-value: 1.68E-10; mr1726_2 (Ind_All); LR P-value: 3.00E-06; mr1739_2 (Ind_All); LR P-value: 5.11E-10; mr1794_2 (Ind_All); LR P-value: 5.91E-11 |
LOC_Os01g02440.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 61.044; most accessible tissue: Callus, score: 84.173 |
| vg0100790495 (J) | chr01 | 790495 | C | T | 39.70% | 43.31% | T -> C | NA |
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02440.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 45.082; most accessible tissue: Callus, score: 77.623 |
| vg0100790572 (J) | chr01 | 790572 | AT | ATTT | 32.80% | 42.89% | AT -> ATT,ATTT,A ,ATTTT | NA |
LOC_Os01g02430.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02460.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02450.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02440.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02430.1 Alt: ATT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02460.1 Alt: ATT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02450.1 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02440.1 Alt: ATT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02430.1 Alt: ATTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02460.1 Alt: ATTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02450.1 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02440.1 Alt: ATTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02430.1 Alt: ATTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02460.1 Alt: ATTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02450.1 Alt: ATTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02440.1 Alt: ATTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 35.988; most accessible tissue: Callus, score: 77.623 |
| vg0100790779 (J) | chr01 | 790779 | G | A | 54.40% | 42.02% | G -> A | NA |
LOC_Os01g02430.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02460.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02450.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02440.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 28.972; most accessible tissue: Callus, score: 77.386 |
| vg0100791115 (J) | chr01 | 791115 | AT | A | 53.50% | 39.82% | AT -> A | NA |
LOC_Os01g02430.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02460.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02450.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02440.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 30.461; most accessible tissue: Zhenshan97 young leaf, score: 47.986 |
| vg0100791132 (J) | chr01 | 791132 | C | A | 54.70% | 41.83% | C -> A | NA |
LOC_Os01g02440.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g02430.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02460.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02450.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 31.120; most accessible tissue: Callus, score: 47.641 |
| vg0100791192 (J) | chr01 | 791192 | C | T | 39.70% | 42.66% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g02430.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02460.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02450.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02440.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 36.057; most accessible tissue: Callus, score: 66.916 |
| vg0100791243 (J) | chr01 | 791243 | G | T | 33.10% | 41.83% | G -> T |
mr1059 (Ind_All); LR P-value: 7.42E-09;
mr1143 (Ind_All); LR P-value: 4.97E-11; mr1167 (Ind_All); LR P-value: 8.83E-10; mr1535 (Ind_All); LR P-value: 1.11E-09; mr1593 (Ind_All); LR P-value: 1.28E-08; mr1675 (Ind_All); LR P-value: 1.22E-09; mr1686 (Ind_All); LR P-value: 8.71E-06; mr1739 (All); LR P-value: 9.90E-08; mr1739 (Ind_All); LR P-value: 1.18E-07; mr1950 (Ind_All); LR P-value: 9.93E-07; mr1969 (Ind_All); LR P-value: 1.11E-09; mr1995 (Ind_All); LR P-value: 2.59E-11; mr1167_2 (Ind_All); LR P-value: 1.68E-08; mr1360_2 (Ind_All); LR P-value: 7.68E-06; mr1378_2 (Ind_All); LR P-value: 2.51E-06; mr1383_2 (Ind_All); LR P-value: 1.74E-07; mr1458_2 (Ind_All); LR P-value: 2.42E-07; mr1593_2 (Ind_All); LR P-value: 5.70E-10; mr1726_2 (Ind_All); LR P-value: 7.05E-06; mr1739_2 (Ind_All); LR P-value: 1.43E-09; mr1794_2 (Ind_All); LR P-value: 2.46E-11 |
LOC_Os01g02430.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02460.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02450.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02440.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 34.858; most accessible tissue: Callus, score: 66.916 |
| vg0100791414 (J) | chr01 | 791414 | G | A | 39.40% | 42.30% | G -> A |
mr1042 (Ind_All); LR P-value: 3.26E-06;
mr1043 (Ind_All); LR P-value: 1.74E-06; mr1050 (Ind_All); LR P-value: 1.84E-06; mr1059 (Ind_All); LR P-value: 2.61E-10; mr1110 (Ind_All); LR P-value: 8.17E-08; mr1143 (Ind_All); LR P-value: 8.76E-14; mr1167 (Ind_All); LR P-value: 3.11E-12; mr1272 (Ind_All); LR P-value: 8.57E-07; mr1291 (All); LR P-value: 3.59E-07; mr1333 (Ind_All); LR P-value: 8.39E-06; mr1399 (Ind_All); LR P-value: 1.98E-06; mr1458 (Ind_All); LR P-value: 2.80E-08; mr1479 (Ind_All); LR P-value: 5.65E-07; mr1502 (Ind_All); LR P-value: 1.01E-06; mr1535 (Ind_All); LR P-value: 4.93E-12; mr1593 (Ind_All); LR P-value: 3.69E-10; mr1608 (Ind_All); LR P-value: 6.44E-06; mr1675 (Ind_All); LR P-value: 4.36E-12; mr1686 (Ind_All); LR P-value: 5.49E-06; mr1726 (Ind_All); LR P-value: 3.03E-09; mr1912 (Ind_All); LR P-value: 4.58E-06; mr1950 (Ind_All); LR P-value: 6.04E-08; mr1969 (Ind_All); LR P-value: 1.46E-12; mr1975 (Ind_All); LR P-value: 4.12E-06; mr1995 (Ind_All); LR P-value: 5.57E-15; mr1110_2 (Ind_All); LR P-value: 7.60E-08; mr1113_2 (Ind_All); LR P-value: 7.53E-06; mr1167_2 (Ind_All); LR P-value: 1.63E-08; mr1195_2 (Ind_All); LR P-value: 5.53E-10; mr1360_2 (Ind_All); LR P-value: 2.12E-06; mr1378_2 (Ind_All); LR P-value: 6.19E-08; mr1383_2 (Ind_All); LR P-value: 6.11E-08; mr1458_2 (Ind_All); LR P-value: 1.33E-08; mr1593_2 (Ind_All); LR P-value: 2.17E-10; mr1726_2 (Ind_All); LR P-value: 5.33E-06; mr1739_2 (Ind_All); LR P-value: 2.60E-09; mr1794_2 (Ind_All); LR P-value: 3.19E-11; mr1895_2 (Ind_All); LR P-value: 3.81E-06 |
LOC_Os01g02440.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 48.560; most accessible tissue: Zhenshan97 panicle, score: 65.386 |
| vg0100791442 (J) | chr01 | 791442 | C | T | 56.70% | 40.20% | C -> T | NA |
LOC_Os01g02440.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 51.277; most accessible tissue: Zhenshan97 panicle, score: 65.386 |
| vg0100791451 (J) | chr01 | 791451 | T | C | 56.60% | 40.27% | T -> C | NA |
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02440.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 51.470; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
| vg0100791452 (J) | chr01 | 791452 | C | T | 56.60% | 40.29% | C -> T | NA |
LOC_Os01g02440.1 Alt: T| missense_variant MODERATE(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 51.470; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
| vg0100791454 (J) | chr01 | 791454 | C | G | 56.50% | 40.25% | C -> G | NA |
LOC_Os01g02440.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 51.470; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
| vg0100791457 (J) | chr01 | 791457 | G | A | 56.40% | 40.25% | G -> A | NA |
LOC_Os01g02440.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 51.640; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
| vg0100791466 (J) | chr01 | 791466 | C | A | 56.30% | 40.31% | C -> A | NA |
LOC_Os01g02440.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 52.900; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
| vg0100791472 (J) | chr01 | 791472 | G | A | 56.20% | 40.48% | G -> A | NA |
LOC_Os01g02440.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 53.570; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
| vg0100791480 (J) | chr01 | 791480 | C | A | 56.30% | 40.41% | C -> A | NA |
LOC_Os01g02440.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 54.274; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0100791484 (J) | chr01 | 791484 | G | A | 56.30% | 40.44% | G -> A | NA |
LOC_Os01g02440.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 54.084; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0100791489 (J) | chr01 | 791489 | G | C | 56.40% | 40.35% | G -> C | NA |
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g02440.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 53.024; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0100791493 (J) | chr01 | 791493 | C | T | 56.30% | 40.37% | C -> T | NA |
LOC_Os01g02440.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 53.225; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0100791504 (J) | chr01 | 791504 | A | G | 69.10% | 19.17% | A -> G | NA |
LOC_Os01g02440.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 52.495; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
| vg0100791512 (J) | chr01 | 791512 | A | T | 55.80% | 40.90% | A -> T | NA |
LOC_Os01g02440.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 52.739; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
| vg0100791519 (J) | chr01 | 791519 | G | A | 49.40% | 26.94% | G -> A |
mr1059 (Ind_All); LR P-value: 5.29E-09;
mr1143 (Ind_All); LR P-value: 3.00E-11; mr1167 (Ind_All); LR P-value: 7.20E-10; mr1535 (Ind_All); LR P-value: 9.56E-10; mr1593 (Ind_All); LR P-value: 5.73E-09; mr1675 (Ind_All); LR P-value: 8.38E-10; mr1726 (Ind_All); LR P-value: 2.11E-07; mr1739 (All); LR P-value: 5.87E-08; mr1739 (Ind_All); LR P-value: 3.48E-08; mr1950 (Ind_All); LR P-value: 6.29E-07; mr1969 (Ind_All); LR P-value: 6.70E-10; mr1995 (Ind_All); LR P-value: 1.39E-11; mr1158_2 (Ind_All); LR P-value: 3.39E-06; mr1167_2 (Ind_All); LR P-value: 8.58E-09; mr1360_2 (Ind_All); LR P-value: 8.52E-06; mr1378_2 (Ind_All); LR P-value: 1.57E-06; mr1383_2 (Ind_All); LR P-value: 5.23E-08; mr1458_2 (Ind_All); LR P-value: 2.72E-07; mr1593_2 (Ind_All); LR P-value: 1.68E-10; mr1726_2 (Ind_All); LR P-value: 3.00E-06; mr1739_2 (Ind_All); LR P-value: 5.11E-10; mr1794_2 (Ind_All); LR P-value: 5.91E-11 |
LOC_Os01g02440.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 53.740; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0100791524 (J) | chr01 | 791524 | AGGG | A | 91.30% | 4.91% | AGGG -> A | NA |
LOC_Os01g02440.1 Alt: A| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 53.902; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0100791529 (J) | chr01 | 791529 | A | ACAT | 55.90% | 40.86% | A -> ACAT | NA |
LOC_Os01g02440.1 Alt: ACAT| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os01g02440.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 54.257; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
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