356 variations found. Os01g0937400/LOC_Os01g71106 (NBS-LRR disease resistance protein; putative; expressed), ranging from 41,155,812 bp to 41,160,726 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g71106 | NBS-LRR disease resistance protein, putative, expressed; RAP ID: Os01g0937400; MSU ID: LOC_Os01g71106 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0141156379 (J) | chr01 | 41156379 | CACGCC | CACGCCA CGCC | 54.10% | 0.00% | CACGCCACGC C -> CACGCC | NA |
|
| STR0141159749 (J) | chr01 | 41159749 | T | C | 86.30% | 0.00% | T -> C | NA |
|
| STR0141160633 (J) | chr01 | 41160633 | C | CTTG | 88.90% | 0.00% | C -> CTTG | NA |
|
| STR0141160700 (J) | chr01 | 41160700 | T | G | 88.90% | 0.00% | T -> G | NA |
|
| vg0141155819 (J) | chr01 | 41155819 | A | T | 92.50% | 5.16% | A -> T | NA |
LOC_Os01g71106.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.615; most accessible tissue: Callus, score: 96.193 |
| vg0141155825 (J) | chr01 | 41155825 | C | T | 92.50% | 5.18% | C -> T | NA |
LOC_Os01g71106.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.470; most accessible tissue: Callus, score: 96.193 |
| vg0141155831 (J) | chr01 | 41155831 | C | T | 92.60% | 5.16% | C -> T | NA |
LOC_Os01g71106.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 85.726; most accessible tissue: Zhenshan97 panicle, score: 92.660 |
| vg0141155832 (J) | chr01 | 41155832 | A | C | 90.80% | 6.86% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g71106.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71100.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.726; most accessible tissue: Zhenshan97 panicle, score: 92.660 |
| vg0141155838 (J) | chr01 | 41155838 | C | T | 90.70% | 5.29% | C -> T | NA |
LOC_Os01g71106.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 85.875; most accessible tissue: Zhenshan97 panicle, score: 92.660 |
| vg0141155840 (J) | chr01 | 41155840 | G | A | 57.80% | 5.63% | A -> G |
LOC_Os01g71106.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 85.919; most accessible tissue: Zhenshan97 panicle, score: 92.660 |
|
| vg0141155855 (J) | chr01 | 41155855 | T | C | 88.90% | 7.11% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g71106.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71100.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.978; most accessible tissue: Zhenshan97 panicle, score: 92.784 |
| vg0141155856 (J) | chr01 | 41155856 | G | C | 83.60% | 7.05% | G -> C,A | NA |
LOC_Os01g71106.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g71106.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71100.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.041; most accessible tissue: Zhenshan97 panicle, score: 92.784 |
| vg0141155860 (J) | chr01 | 41155860 | CGGGGT | C | 47.00% | 5.59% | C -> CGGGGT,T,C GAGGT,CA | NA |
LOC_Os01g71106.2 Alt: CA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71106.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71100.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g71106.2 Alt: CGAGGT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71100.1 Alt: CGAGGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: CGAGGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71106.2 Alt: CGGGGT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71100.1 Alt: CGGGGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: CGGGGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.184; most accessible tissue: Zhenshan97 panicle, score: 92.904 |
| vg0141155861 (J) | chr01 | 41155861 | G | A | 45.90% | 38.26% | G -> A |
mr1126 (All); LR P-value: 2.54E-08;
mr1207 (All); LR P-value: 4.81E-06; mr1210 (All); LR P-value: 2.67E-23; mr1231 (All); LR P-value: 4.08E-14; mr1244 (All); LR P-value: 3.86E-20; mr1305 (All); LR P-value: 2.06E-25; mr1369 (All); LR P-value: 4.06E-07; mr1382 (All); LR P-value: 2.11E-06; mr1403 (All); LR P-value: 3.89E-08; mr1409 (All); LR P-value: 1.67E-12; mr1453 (All); LR P-value: 3.77E-07; mr1465 (All); LR P-value: 7.70E-09; mr1522 (All); LR P-value: 7.80E-12; mr1523 (All); LR P-value: 5.86E-06; mr1586 (All); LR P-value: 3.22E-25; mr1633 (All); LR P-value: 9.44E-06; mr1652 (All); LR P-value: 1.08E-06; mr1669 (All); LR P-value: 9.33E-08; mr1696 (All); LR P-value: 9.20E-11; mr1765 (All); LR P-value: 4.57E-17; mr1889_2 (All); LMM P-value: 2.41E-06 |
LOC_Os01g71106.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.255; most accessible tissue: Zhenshan97 panicle, score: 92.904 |
| vg0141155864 (J) | chr01 | 41155864 | G | A | 92.60% | 5.12% | G -> A | NA |
LOC_Os01g71106.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.100; most accessible tissue: Zhenshan97 panicle, score: 92.904 |
| vg0141155866 (J) | chr01 | 41155866 | A | G | 92.60% | 5.12% | A -> G | NA |
LOC_Os01g71106.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.162; most accessible tissue: Zhenshan97 panicle, score: 92.904 |
| vg0141155869 (J) | chr01 | 41155869 | G | A | 92.70% | 5.12% | G -> A | NA |
LOC_Os01g71106.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.331; most accessible tissue: Zhenshan97 panicle, score: 93.020 |
| vg0141155873 (J) | chr01 | 41155873 | C | A | 92.70% | 5.12% | C -> A | NA |
LOC_Os01g71106.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.702; most accessible tissue: Zhenshan97 panicle, score: 93.244 |
| vg0141155876 (J) | chr01 | 41155876 | C | T | 90.50% | 5.21% | C -> T |
mr1262 (All); LR P-value: 1.98E-06;
mr1549 (All); LR P-value: 9.69E-42; mr1550 (All); LR P-value: 7.65E-49; mr1757 (All); LR P-value: 1.46E-42; mr1931 (All); LR P-value: 3.34E-06; mr1134_2 (All); LMM P-value: 1.47E-06; mr1510_2 (All); LR P-value: 2.41E-08; mr1530_2 (All); LR P-value: 4.50E-15; mr1549_2 (All); LR P-value: 4.22E-31; mr1550_2 (All); LR P-value: 2.09E-48; mr1740_2 (All); LR P-value: 8.72E-06; mr1757_2 (All); LR P-value: 3.85E-28 |
LOC_Os01g71106.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.416; most accessible tissue: Zhenshan97 panicle, score: 93.133 |
| vg0141155880 (J) | chr01 | 41155880 | G | A | 94.20% | 5.27% | G -> A | NA |
LOC_Os01g71106.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.057; most accessible tissue: Zhenshan97 panicle, score: 93.133 |
| vg0141155884 (J) | chr01 | 41155884 | A | G | 54.10% | 5.73% | G -> A |
LOC_Os01g71106.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 85.871; most accessible tissue: Zhenshan97 panicle, score: 93.020 |
|
| vg0141155885 (J) | chr01 | 41155885 | G | A | 88.80% | 5.23% | G -> A |
mr1262 (All); LR P-value: 6.40E-07;
mr1286 (All); LR P-value: 2.34E-06; mr1287 (All); LR P-value: 6.15E-06; mr1345 (All); LR P-value: 3.98E-06; mr1353 (All); LR P-value: 2.15E-06; mr1372 (All); LR P-value: 2.07E-06; mr1382 (All); LR P-value: 3.93E-06; mr1417 (All); LR P-value: 9.55E-06; mr1906 (All); LR P-value: 9.37E-06; mr1939 (All); LR P-value: 1.74E-09 |
LOC_Os01g71106.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 85.839; most accessible tissue: Zhenshan97 panicle, score: 93.020 |
| vg0141155903 (J) | chr01 | 41155903 | AT | A | 92.70% | 5.04% | AT -> A | NA |
LOC_Os01g71106.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.461; most accessible tissue: Zhenshan97 panicle, score: 93.020 |
| vg0141155907 (J) | chr01 | 41155907 | A | G | 90.40% | 5.18% | A -> G | NA |
LOC_Os01g71106.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 86.386; most accessible tissue: Zhenshan97 panicle, score: 92.904 |
| vg0141155910 (J) | chr01 | 41155910 | A | G | 90.90% | 5.16% | A -> G | NA |
LOC_Os01g71106.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g71100.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g71114.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 87.152; most accessible tissue: Zhenshan97 panicle, score: 93.020 |
Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China
Comments or Questions? Please contact us. Our website: http://xielab.ncpgr.cn/