58 variations found. LOC_Os03g49640 (STE_MEKK_ste11_MAP3K.14 - STE kinases include homologs to sterile 7; sterile 11 and sterile 20 from yeast; expressed), ranging from 28,269,517 bp to 28,275,709 bp (including 0 kb upstream and 0 kb downstream of the gene).
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0328274591 (J) | chr03 | 28274591 | CTCC | C | 61.40% | 0.00% | CTCCTCC -> C,CTCC | NA |
|
| vg0328269655 (J) | chr03 | 28269655 | A | T | 99.90% | 0.00% | A -> T | NA |
LOC_Os03g49640.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g49640.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g49630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g49630.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.036; most accessible tissue: Zhenshan97 flag leaf, score: 93.395 |
| vg0328269738 (J) | chr03 | 28269738 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os03g49640.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49640.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49630.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.036; most accessible tissue: Zhenshan97 flag leaf, score: 91.379 |
| vg0328269877 (J) | chr03 | 28269877 | A | T | 99.80% | 0.00% | A -> T | NA |
LOC_Os03g49640.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g49640.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g49630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g49630.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.728; most accessible tissue: Minghui63 flag leaf, score: 90.593 |
| vg0328270045 (J) | chr03 | 28270045 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g49640.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g49640.2 Alt: A| missense_variant MODERATE(snpEff) LOC_Os03g49630.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g49630.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 68.945; most accessible tissue: Minghui63 flag leaf, score: 85.500 |
| vg0328270416 (J) | chr03 | 28270416 | A | G | 65.40% | 0.17% | G -> A | NA |
LOC_Os03g49630.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49630.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 54.128; most accessible tissue: Minghui63 flower, score: 75.921 |
| vg0328270664 (J) | chr03 | 28270664 | C | A | 99.10% | 0.00% | C -> A | NA |
LOC_Os03g49630.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g49630.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g49640.1 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os03g49640.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 48.606; most accessible tissue: Minghui63 flower, score: 71.461 |
| vg0328270702 (J) | chr03 | 28270702 | GGT | G | 90.60% | 0.00% | GGT -> G | NA |
LOC_Os03g49630.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49630.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.039; most accessible tissue: Callus, score: 80.558 |
| vg0328270720 (J) | chr03 | 28270720 | A | G | 65.50% | 0.15% | G -> A | NA |
LOC_Os03g49630.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49630.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 48.883; most accessible tissue: Callus, score: 80.558 |
| vg0328270750 (J) | chr03 | 28270750 | A | AT | 99.70% | 0.00% | A -> AT | NA |
LOC_Os03g49630.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49630.2 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.2 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 50.075; most accessible tissue: Callus, score: 80.558 |
| vg0328270847 (J) | chr03 | 28270847 | A | T | 86.40% | 0.00% | A -> T |
mr1004 (All); LR P-value: 7.63E-06;
mr1006 (All); LR P-value: 3.49E-06; mr1042 (Ind_All); LR P-value: 6.28E-06; mr1043 (Ind_All); LR P-value: 2.13E-06; mr1052 (All); LR P-value: 4.06E-06; mr1073 (All); LR P-value: 1.06E-06; mr1331 (All); LR P-value: 9.80E-06; mr1369 (All); LR P-value: 9.65E-07; mr1397 (All); LR P-value: 2.63E-06; mr1502 (Ind_All); LR P-value: 2.26E-06; mr1662 (All); LR P-value: 1.39E-09; mr1662 (Ind_All); LR P-value: 2.23E-06; mr1764 (All); LR P-value: 6.01E-07; mr1817 (All); LR P-value: 2.58E-20; mr1912 (Ind_All); LR P-value: 2.61E-06; mr1193_2 (All); LR P-value: 3.35E-11; mr1219_2 (All); LR P-value: 8.89E-06 |
LOC_Os03g49630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49630.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 41.470; most accessible tissue: Zhenshan97 flag leaf, score: 65.820 |
| vg0328270852 (J) | chr03 | 28270852 | A | G | 51.50% | 0.04% | G -> A |
mr1013 (All); LR P-value: 2.22E-13;
mr1219 (Ind_All); LR P-value: 2.54E-06; mr1325 (Ind_All); LR P-value: 3.37E-06; mr1379 (All); LR P-value: 1.43E-09; mr1662 (Ind_All); LR P-value: 1.87E-06; mr1717 (All); LR P-value: 7.49E-07; mr1745 (All); LR P-value: 1.40E-32; mr1804 (All); LR P-value: 1.03E-07; mr1827 (All); LR P-value: 2.44E-08; mr1219_2 (Ind_All); LR P-value: 2.49E-07 |
LOC_Os03g49630.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49630.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 41.629; most accessible tissue: Zhenshan97 flag leaf, score: 65.820 |
| vg0328270924 (J) | chr03 | 28270924 | G | T | 99.80% | 0.00% | G -> T | NA |
LOC_Os03g49630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g49630.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os03g49640.1 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os03g49640.2 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 41.025; most accessible tissue: Minghui63 flag leaf, score: 60.569 |
| vg0328271042 (J) | chr03 | 28271042 | C | A | 65.60% | 0.00% | A -> C | NA |
LOC_Os03g49630.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49630.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 50.478; most accessible tissue: Callus, score: 77.833 |
| vg0328271061 (J) | chr03 | 28271061 | C | T | 65.50% | 0.25% | T -> C | NA |
LOC_Os03g49630.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49630.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 49.756; most accessible tissue: Callus, score: 77.833 |
| vg0328271496 (J) | chr03 | 28271496 | G | GCAT | 99.60% | 0.00% | G -> GCAT | NA |
LOC_Os03g49640.1 Alt: GCAT| intron_variant MODIFIER(snpEff)
LOC_Os03g49640.2 Alt: GCAT| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 42.388; most accessible tissue: Zhenshan97 flag leaf, score: 68.703 |
| vg0328271525 (J) | chr03 | 28271525 | CAA | C | 52.70% | 0.00% | C -> CAA,CA,CAA A | NA |
LOC_Os03g49640.1 Alt: CAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49640.2 Alt: CAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.1 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.2 Alt: CAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.1 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.2 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 45.322; most accessible tissue: Zhenshan97 flag leaf, score: 73.119 |
| vg0328271536 (J) | chr03 | 28271536 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g49640.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os03g49640.2 Alt: A| splice_region_variant&intron_variant LOW(snpEff) The average chromatin accessibility score: 42.242; most accessible tissue: Zhenshan97 flag leaf, score: 69.582 |
| vg0328271674 (J) | chr03 | 28271674 | T | C | 65.20% | 0.00% | C -> T | NA |
LOC_Os03g49640.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49640.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 50.856; most accessible tissue: Minghui63 flag leaf, score: 74.955 |
| vg0328271771 (J) | chr03 | 28271771 | G | A | 99.00% | 0.00% | G -> A | NA |
LOC_Os03g49640.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49640.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.543; most accessible tissue: Callus, score: 79.100 |
| vg0328271784 (J) | chr03 | 28271784 | C | A | 65.50% | 0.08% | A -> C | NA |
LOC_Os03g49640.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49640.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 57.777; most accessible tissue: Callus, score: 79.100 |
| vg0328272110 (J) | chr03 | 28272110 | G | A | 97.60% | 0.00% | G -> A | NA |
LOC_Os03g49640.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g49640.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 54.103; most accessible tissue: Minghui63 flag leaf, score: 71.577 |
| vg0328272292 (J) | chr03 | 28272292 | GA | G | 64.30% | 0.15% | G -> GA,GAA | NA |
LOC_Os03g49640.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49640.2 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os03g49640.1 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g49640.2 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.292; most accessible tissue: Callus, score: 78.091 |
| vg0328272347 (J) | chr03 | 28272347 | C | T | 51.50% | 0.34% | T -> C |
mr1013 (All); LR P-value: 3.18E-13;
mr1219 (Ind_All); LR P-value: 1.82E-06; mr1325 (Ind_All); LR P-value: 7.23E-06; mr1662 (Ind_All); LR P-value: 4.98E-07; mr1745 (All); LR P-value: 5.57E-33; mr1804 (All); LR P-value: 9.13E-08; mr1827 (All); LR P-value: 1.75E-08; mr1219_2 (Ind_All); LR P-value: 1.85E-07; mr1662_2 (Ind_All); LR P-value: 9.04E-06; mr1745_2 (All); LR P-value: 1.04E-38 |
LOC_Os03g49640.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49640.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 54.101; most accessible tissue: Minghui63 flag leaf, score: 76.091 |
| vg0328272522 (J) | chr03 | 28272522 | G | T | 96.00% | 0.00% | G -> T |
mr1043 (Ind_All); LR P-value: 6.38E-06;
mr1201 (All); LR P-value: 5.20E-07; mr1201 (Ind_All); LR P-value: 8.71E-07; mr1219 (Ind_All); LR P-value: 1.50E-06; mr1274 (All); LR P-value: 8.68E-07; mr1291 (Ind_All); LR P-value: 4.49E-06; mr1502 (All); LR P-value: 1.42E-07; mr1502 (Ind_All); LR P-value: 1.51E-07; mr1662 (All); LR P-value: 8.05E-09; mr1662 (Ind_All); LR P-value: 4.09E-09; mr1677 (Ind_All); LR P-value: 2.52E-06; mr1745 (Ind_All); LR P-value: 7.75E-07; mr1201_2 (All); LR P-value: 8.87E-09; mr1201_2 (Ind_All); LR P-value: 2.34E-08; mr1219_2 (All); LR P-value: 5.22E-07; mr1219_2 (Ind_All); LR P-value: 2.18E-08; mr1274_2 (All); LR P-value: 1.44E-06; mr1662_2 (All); LR P-value: 3.80E-07; mr1662_2 (Ind_All); LR P-value: 5.13E-07; mr1745_2 (Ind_All); LR P-value: 9.91E-06 |
LOC_Os03g49640.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g49640.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.444; most accessible tissue: Callus, score: 77.231 |
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