21 variations found. Os09g0473966/LOC_Os09g29800 (expressed protein), ranging from 18,111,329 bp to 18,113,596 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os09g29800 | hypothetical protein; RAP ID: Os09g0473966; MSU ID: LOC_Os09g29800 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0918111479 (J) | chr09 | 18111479 | T | C | 64.20% | 0.00% | C -> T |
mr1175 (All); LR P-value: 5.35E-10;
mr1219 (Ind_All); LR P-value: 1.17E-07; mr1274 (Ind_All); LR P-value: 5.98E-07; mr1342 (All); LR P-value: 1.08E-08; mr1676 (All); LR P-value: 4.74E-20; mr1006_2 (Ind_All); LR P-value: 2.37E-06; mr1097_2 (All); LR P-value: 2.91E-12; mr1201_2 (Ind_All); LR P-value: 1.07E-06; mr1219_2 (Ind_All); LR P-value: 4.47E-10; mr1274_2 (Ind_All); LR P-value: 5.27E-07; mr1377_2 (All); LR P-value: 1.45E-11; mr1637_2 (All); LR P-value: 7.80E-20 |
LOC_Os09g29790.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29810.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.881; most accessible tissue: Zhenshan97 flower, score: 94.175 |
| vg0918111497 (J) | chr09 | 18111497 | C | T | 97.60% | 0.00% | C -> T |
LOC_Os09g29790.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29810.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.748; most accessible tissue: Minghui63 root, score: 93.921 |
|
| vg0918111643 (J) | chr09 | 18111643 | GAGG | CAGG | 63.10% | 0.00% | CAGG -> GAGG,C |
mr1201 (Ind_All); LR P-value: 3.31E-06;
mr1219 (Ind_All); LR P-value: 3.87E-08; mr1243 (All); LR P-value: 3.22E-31; mr1274 (Ind_All); LR P-value: 1.71E-07; mr1342 (All); LR P-value: 9.60E-09; mr1733 (All); LR P-value: 6.62E-33; mr1006_2 (Ind_All); LR P-value: 2.52E-06; mr1201_2 (Ind_All); LR P-value: 1.63E-07; mr1219_2 (Ind_All); LR P-value: 1.20E-10; mr1274_2 (Ind_All); LR P-value: 1.31E-07; mr1637_2 (All); LR P-value: 1.30E-18 |
LOC_Os09g29790.1 Alt: GAGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29810.1 Alt: GAGG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: GAGG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29790.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29810.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.449; most accessible tissue: Zhenshan97 flower, score: 92.326 |
| vg0918111646 (J) | chr09 | 18111646 | G | C | 96.70% | 0.00% | G -> C |
LOC_Os09g29790.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29810.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.418; most accessible tissue: Zhenshan97 flower, score: 92.326 |
|
| vg0918111800 (J) | chr09 | 18111800 | CTTTT | CTTT | 40.70% | 0.00% | CTTTT -> C,CT,CTTT, CTT,CTTTTT | NA |
LOC_Os09g29790.1 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29810.1 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29790.1 Alt: CTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29810.1 Alt: CTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: CTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29790.1 Alt: CTTTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29810.1 Alt: CTTTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: CTTTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29790.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g29810.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g29800.1 Alt: C| intron_variant MODIFIER(snpEff) LOC_Os09g29790.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29810.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: CT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.205; most accessible tissue: Callus, score: 84.784 |
| vg0918111959 (J) | chr09 | 18111959 | G | A | 64.40% | 0.00% | A -> G |
mr1175 (All); LR P-value: 4.58E-10;
mr1219 (Ind_All); LR P-value: 1.33E-07; mr1274 (Ind_All); LR P-value: 6.81E-07; mr1342 (All); LR P-value: 9.45E-09; mr1676 (All); LR P-value: 4.19E-20; mr1006_2 (Ind_All); LR P-value: 2.47E-06; mr1097_2 (All); LR P-value: 4.31E-12; mr1201_2 (Ind_All); LR P-value: 1.27E-06; mr1219_2 (Ind_All); LR P-value: 5.26E-10; mr1274_2 (Ind_All); LR P-value: 6.06E-07; mr1377_2 (All); LR P-value: 1.19E-11; mr1637_2 (All); LR P-value: 5.08E-20; mr1705_2 (All); LR P-value: 5.10E-09 |
LOC_Os09g29790.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29810.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 73.094; most accessible tissue: Callus, score: 85.965 |
| vg0918112154 (J) | chr09 | 18112154 | AT | A | 66.30% | 0.06% | A -> AT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g29790.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29810.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.456; most accessible tissue: Zhenshan97 panicle, score: 72.468 |
| vg0918112167 (J) | chr09 | 18112167 | A | C | 64.40% | 0.00% | C -> A |
mr1175 (All); LR P-value: 4.58E-10;
mr1219 (Ind_All); LR P-value: 1.33E-07; mr1274 (Ind_All); LR P-value: 6.81E-07; mr1342 (All); LR P-value: 9.45E-09; mr1676 (All); LR P-value: 4.19E-20; mr1006_2 (Ind_All); LR P-value: 2.47E-06; mr1097_2 (All); LR P-value: 4.31E-12; mr1201_2 (Ind_All); LR P-value: 1.27E-06; mr1219_2 (Ind_All); LR P-value: 5.26E-10; mr1274_2 (Ind_All); LR P-value: 6.06E-07; mr1377_2 (All); LR P-value: 1.19E-11; mr1637_2 (All); LR P-value: 5.08E-20; mr1705_2 (All); LR P-value: 5.10E-09 |
LOC_Os09g29790.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29810.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 52.172; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
| vg0918112495 (J) | chr09 | 18112495 | AT | A | 99.00% | 0.00% | AT -> A,ATT | NA |
LOC_Os09g29790.1 Alt: ATT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29810.1 Alt: ATT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: ATT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29790.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29810.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.090; most accessible tissue: Callus, score: 80.523 |
| vg0918112508 (J) | chr09 | 18112508 | T | A | 63.90% | 0.00% | A -> T |
mr1175 (All); LR P-value: 7.31E-10;
mr1201 (Ind_All); LR P-value: 3.31E-06; mr1219 (Ind_All); LR P-value: 3.87E-08; mr1243 (All); LR P-value: 5.15E-31; mr1274 (Ind_All); LR P-value: 1.71E-07; mr1733 (All); LR P-value: 7.31E-33; mr1006_2 (Ind_All); LR P-value: 2.52E-06; mr1097_2 (All); LR P-value: 1.75E-11; mr1201_2 (Ind_All); LR P-value: 1.63E-07; mr1219_2 (Ind_All); LR P-value: 1.20E-10; mr1274_2 (Ind_All); LR P-value: 1.31E-07; mr1637_2 (All); LR P-value: 2.18E-19 |
LOC_Os09g29790.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29810.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 34.970; most accessible tissue: Callus, score: 80.523 |
| vg0918112528 (J) | chr09 | 18112528 | C | T | 57.00% | 0.00% | C -> T |
mr1138 (All); LR P-value: 4.11E-15;
mr1138 (Ind_All); LR P-value: 2.05E-08; mr1716 (All); LR P-value: 3.47E-07; mr1728 (Ind_All); LR P-value: 9.34E-08; mr1860 (Ind_All); LR P-value: 2.24E-06; mr1138_2 (All); LR P-value: 4.20E-15; mr1138_2 (Ind_All); LR P-value: 4.33E-08; mr1330_2 (All); LR P-value: 4.49E-14; mr1352_2 (All); LR P-value: 4.99E-18; mr1527_2 (All); LR P-value: 6.38E-09; mr1728_2 (Ind_All); LR P-value: 1.50E-08; mr1834_2 (All); LR P-value: 5.25E-07; mr1860_2 (Ind_All); LR P-value: 3.93E-07 |
LOC_Os09g29790.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29810.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 35.513; most accessible tissue: Callus, score: 80.523 |
| vg0918112664 (J) | chr09 | 18112664 | A | C | 63.90% | 0.00% | C -> A |
mr1219 (Ind_All); LR P-value: 1.01E-07;
mr1274 (Ind_All); LR P-value: 3.52E-07; mr1342 (All); LR P-value: 6.54E-09; mr1006_2 (Ind_All); LR P-value: 2.39E-06; mr1097_2 (All); LR P-value: 7.58E-12; mr1201_2 (Ind_All); LR P-value: 6.20E-07; mr1219_2 (Ind_All); LR P-value: 6.04E-10; mr1274_2 (Ind_All); LR P-value: 5.05E-07 |
LOC_Os09g29790.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29810.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 26.953; most accessible tissue: Callus, score: 58.491 |
| vg0918112943 (J) | chr09 | 18112943 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os09g29790.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g29810.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g29800.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 27.756; most accessible tissue: Callus, score: 67.601 |
| vg0918112967 (J) | chr09 | 18112967 | T | C | 64.00% | 0.00% | C -> T |
mr1011 (All); LR P-value: 8.22E-06;
mr1219 (Ind_All); LR P-value: 1.17E-07; mr1274 (Ind_All); LR P-value: 5.98E-07; mr1006_2 (Ind_All); LR P-value: 2.37E-06; mr1097_2 (All); LR P-value: 2.09E-11; mr1201_2 (Ind_All); LR P-value: 1.07E-06; mr1219_2 (Ind_All); LR P-value: 4.47E-10; mr1274_2 (Ind_All); LR P-value: 5.27E-07; mr1636_2 (All); LR P-value: 8.58E-12; mr1637_2 (All); LR P-value: 7.21E-20 |
LOC_Os09g29800.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 29.367; most accessible tissue: Callus, score: 67.601 |
| vg0918113312 (J) | chr09 | 18113312 | T | TA | 92.20% | 0.00% | T -> TA | NA |
LOC_Os09g29790.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29810.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 36.525; most accessible tissue: Callus, score: 71.857 |
| vg0918113376 (J) | chr09 | 18113376 | A | T | 64.30% | 0.00% | T -> A |
mr1011 (All); LR P-value: 5.79E-06;
mr1175 (All); LR P-value: 6.35E-10; mr1201 (Ind_All); LR P-value: 3.31E-06; mr1219 (Ind_All); LR P-value: 3.87E-08; mr1274 (Ind_All); LR P-value: 1.71E-07; mr1342 (All); LR P-value: 1.52E-08; mr1006_2 (Ind_All); LR P-value: 2.52E-06; mr1097_2 (All); LR P-value: 3.21E-12; mr1201_2 (Ind_All); LR P-value: 1.63E-07; mr1219_2 (Ind_All); LR P-value: 1.20E-10; mr1274_2 (Ind_All); LR P-value: 1.31E-07; mr1636_2 (All); LR P-value: 1.50E-11; mr1637_2 (All); LR P-value: 2.61E-19 |
LOC_Os09g29800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 34.274; most accessible tissue: Callus, score: 55.626 |
| vg0918113380 (J) | chr09 | 18113380 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os09g29800.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os09g29790.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g29810.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 34.525; most accessible tissue: Callus, score: 55.626 |
| vg0918113486 (J) | chr09 | 18113486 | A | G | 64.30% | 0.08% | G -> A |
mr1175 (All); LR P-value: 4.58E-10;
mr1219 (Ind_All); LR P-value: 1.33E-07; mr1274 (Ind_All); LR P-value: 6.81E-07; mr1342 (All); LR P-value: 9.45E-09; mr1676 (All); LR P-value: 4.19E-20; mr1006_2 (Ind_All); LR P-value: 2.47E-06; mr1097_2 (All); LR P-value: 4.31E-12; mr1201_2 (Ind_All); LR P-value: 1.27E-06; mr1219_2 (Ind_All); LR P-value: 5.26E-10; mr1274_2 (Ind_All); LR P-value: 6.06E-07; mr1377_2 (All); LR P-value: 1.19E-11; mr1637_2 (All); LR P-value: 5.08E-20; mr1705_2 (All); LR P-value: 5.10E-09 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g29790.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29810.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 35.512; most accessible tissue: Callus, score: 75.372 |
| vg0918113499 (J) | chr09 | 18113499 | A | T | 80.50% | 0.00% | A -> T |
mr1138 (Ind_All); LR P-value: 2.91E-09;
mr1707 (Ind_All); LR P-value: 4.05E-07; mr1728 (All); LMM P-value: 5.07E-06; LR P-value: 5.66E-10; mr1728 (Ind_All); LMM P-value: 1.41E-06; LR P-value: 2.96E-12; mr1860 (Ind_All); LR P-value: 8.13E-09; mr1008_2 (Ind_All); LR P-value: 1.93E-06; mr1138_2 (Ind_All); LR P-value: 9.77E-09; mr1707_2 (All); LMM P-value: 4.42E-06; mr1707_2 (Ind_All); LMM P-value: 4.34E-07; LR P-value: 7.73E-08; mr1728_2 (All); LMM P-value: 1.86E-06; mr1728_2 (Ind_All); LMM P-value: 4.71E-07; LR P-value: 1.58E-13; mr1860_2 (Ind_All); LR P-value: 1.36E-10 |
LOC_Os09g29790.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29810.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29800.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 36.184; most accessible tissue: Callus, score: 75.372 |
| vg0918113528 (J) | chr09 | 18113528 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os09g29790.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g29810.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g29800.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 36.945; most accessible tissue: Callus, score: 75.372 |
| STR0918112155 (J) | chr09 | 18112155 | TTT | TT | 65.80% | 0.00% | TT -> TTT | NA |
|