57 variations found. Os09g0475400/LOC_Os09g29930 (transcription factor BIM2; putative; expressed), ranging from 18,207,612 bp to 18,215,108 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os09g29930 | transcription factor BIM2, putative, expressed; RAP ID: Os09g0475400; MSU ID: LOC_Os09g29930 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0918214270 (J) | chr09 | 18214270 | CCC | C | 56.50% | 0.00% | C -> CCC | NA |
|
| vg0918208007 (J) | chr09 | 18208007 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os09g29930.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os09g29930.3 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g29930.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 95.329; most accessible tissue: Zhenshan97 flower, score: 99.721 |
| vg0918208103 (J) | chr09 | 18208103 | A | T | 99.20% | 0.00% | A -> T | NA |
LOC_Os09g29930.1 Alt: T| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 94.554; most accessible tissue: Zhenshan97 flower, score: 99.554 |
| vg0918208109 (J) | chr09 | 18208109 | GA | GAA | 99.10% | 0.00% | GA -> G,GAA | NA |
LOC_Os09g29930.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os09g29930.3 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g29930.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g29930.1 Alt: GAA| splice_region_variant&intron_variant LOW(snpEff) LOC_Os09g29930.3 Alt: GAA| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g29930.2 Alt: GAA| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.547; most accessible tissue: Zhenshan97 flower, score: 99.529 |
| vg0918208120 (J) | chr09 | 18208120 | C | A | 99.60% | 0.00% | C -> A | NA |
LOC_Os09g29930.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29930.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.682; most accessible tissue: Zhenshan97 flower, score: 99.530 |
| vg0918208132 (J) | chr09 | 18208132 | G | T | 99.70% | 0.00% | G -> T | NA |
LOC_Os09g29930.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g29930.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g29930.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.819; most accessible tissue: Zhenshan97 flower, score: 99.540 |
| vg0918208183 (J) | chr09 | 18208183 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os09g29930.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g29930.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g29930.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.155; most accessible tissue: Zhenshan97 flower, score: 99.360 |
| vg0918208280 (J) | chr09 | 18208280 | AG | A | 40.00% | 43.17% | AG -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g29930.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.596; most accessible tissue: Minghui63 flower, score: 99.413 |
| vg0918208289 (J) | chr09 | 18208289 | GA | G | 55.90% | 0.00% | G -> GA | NA |
LOC_Os09g29930.3 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29930.2 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.704; most accessible tissue: Minghui63 flower, score: 99.452 |
| vg0918208342 (J) | chr09 | 18208342 | C | A | 99.70% | 0.00% | C -> A | NA |
LOC_Os09g29930.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29930.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.052; most accessible tissue: Zhenshan97 flower, score: 99.701 |
| vg0918208533 (J) | chr09 | 18208533 | T | C | 55.80% | 0.04% | C -> T |
mr1011 (All); LR P-value: 7.49E-06;
mr1138 (All); LR P-value: 2.58E-14; mr1138 (Ind_All); LR P-value: 4.27E-09; mr1193 (All); LR P-value: 4.35E-07; mr1518 (All); LR P-value: 1.75E-18; mr1637 (All); LR P-value: 3.38E-09; mr1707 (Ind_All); LR P-value: 1.73E-06; mr1728 (Ind_All); LR P-value: 2.19E-11; mr1804 (All); LR P-value: 4.40E-07; mr1860 (Ind_All); LR P-value: 9.43E-08; mr1138_2 (All); LR P-value: 2.27E-14; mr1138_2 (Ind_All); LR P-value: 3.99E-08; mr1636_2 (All); LR P-value: 1.44E-11; mr1707_2 (All); LMM P-value: 9.11E-06; mr1707_2 (Ind_All); LR P-value: 4.79E-06; mr1728_2 (Ind_All); LR P-value: 1.05E-11; mr1860_2 (Ind_All); LR P-value: 5.85E-08 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g29930.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.572; most accessible tissue: Zhenshan97 flower, score: 99.851 |
| vg0918208683 (J) | chr09 | 18208683 | G | A | 55.80% | 0.00% | A -> G | NA |
LOC_Os09g29930.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 99.301; most accessible tissue: Zhenshan97 flag leaf, score: 99.786 |
| vg0918208705 (J) | chr09 | 18208705 | T | TGCA | 45.30% | 0.00% | T -> TGCA,TGCAG CTGCA | NA |
LOC_Os09g29930.1 Alt: TGCA| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os09g29930.1 Alt: TGCAGCTGCA| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 99.340; most accessible tissue: Zhenshan97 flag leaf, score: 99.846 |
| vg0918208836 (J) | chr09 | 18208836 | C | CCCGCCG | 99.20% | 0.00% | C -> CCCGCCG | NA |
LOC_Os09g29930.1 Alt: CCCGCCG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 97.525; most accessible tissue: Zhenshan97 flag leaf, score: 99.911 |
| vg0918208915 (J) | chr09 | 18208915 | G | T | 99.60% | 0.00% | G -> T | NA |
LOC_Os09g29930.3 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g29930.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g29930.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.716; most accessible tissue: Zhenshan97 flag leaf, score: 99.960 |
| vg0918209026 (J) | chr09 | 18209026 | CACGCGG CCACGCG T | CT | 55.60% | 0.00% | CT -> CACGCGGCCA CGCGT,C | NA |
LOC_Os09g29930.3 Alt: CACGCGGCCACGCGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29930.2 Alt: CACGCGGCCACGCGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.1 Alt: CACGCGGCCACGCGT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.3 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.832; most accessible tissue: Zhenshan97 flag leaf, score: 99.988 |
| vg0918209028 (J) | chr09 | 18209028 | G | A | 57.40% | 29.37% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g29930.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.836; most accessible tissue: Zhenshan97 flag leaf, score: 99.989 |
| vg0918209291 (J) | chr09 | 18209291 | A | G | 55.80% | 0.00% | G -> A |
mr1011 (All); LR P-value: 7.66E-06;
mr1138 (All); LR P-value: 3.22E-13; mr1138 (Ind_All); LR P-value: 4.27E-09; mr1193 (All); LR P-value: 1.99E-07; mr1637 (All); LR P-value: 8.49E-09; mr1707 (Ind_All); LR P-value: 1.73E-06; mr1728 (Ind_All); LR P-value: 2.19E-11; mr1860 (Ind_All); LR P-value: 9.43E-08; mr1138_2 (All); LR P-value: 1.69E-13; mr1138_2 (Ind_All); LR P-value: 3.99E-08; mr1636_2 (All); LR P-value: 8.42E-12; mr1707_2 (Ind_All); LR P-value: 4.79E-06; mr1728_2 (All); LMM P-value: 7.18E-06; mr1728_2 (Ind_All); LR P-value: 1.05E-11; mr1860_2 (Ind_All); LR P-value: 5.85E-08 |
LOC_Os09g29930.3 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29930.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.971; most accessible tissue: Zhenshan97 flower, score: 99.991 |
| vg0918209417 (J) | chr09 | 18209417 | G | A | 55.70% | 0.00% | A -> G |
mr1138 (All); LR P-value: 2.80E-13;
mr1138 (Ind_All); LR P-value: 8.58E-09; mr1193 (All); LR P-value: 1.48E-07; mr1291 (All); LR P-value: 1.76E-06; mr1408 (All); LR P-value: 3.97E-06; mr1518 (All); LR P-value: 1.92E-18; mr1518 (Ind_All); LR P-value: 3.38E-06; mr1637 (All); LR P-value: 8.79E-09; mr1676 (Ind_All); LR P-value: 5.22E-06; mr1693 (All); LR P-value: 6.79E-09; mr1707 (Ind_All); LR P-value: 1.80E-06; mr1728 (Ind_All); LR P-value: 3.61E-11; mr1860 (Ind_All); LR P-value: 1.60E-07; mr1138_2 (All); LR P-value: 2.03E-13; mr1138_2 (Ind_All); LR P-value: 1.54E-07; mr1369_2 (All); LR P-value: 2.62E-06; mr1636_2 (All); LR P-value: 5.53E-12; mr1641_2 (All); LR P-value: 8.21E-12; mr1683_2 (All); LR P-value: 2.94E-07; mr1728_2 (All); LMM P-value: 4.95E-06; mr1728_2 (Ind_All); LR P-value: 2.28E-11; mr1860_2 (Ind_All); LR P-value: 2.27E-07 |
LOC_Os09g29930.3 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29930.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.829; most accessible tissue: Zhenshan97 panicle, score: 99.973 |
| vg0918209461 (J) | chr09 | 18209461 | G | GCACCAC | 45.50% | 0.00% | G -> GCACCAC,GC AC,GCACCAC CACCACCACC AC,GCACCAC CAC | NA |
LOC_Os09g29930.1 Alt: GCACCACCACCACCACCAC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os09g29930.1 Alt: GCACCAC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os09g29930.1 Alt: GCACCACCAC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os09g29930.1 Alt: GCAC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 99.862; most accessible tissue: Zhenshan97 panicle, score: 99.958 |
| vg0918209546 (J) | chr09 | 18209546 | A | T | 55.80% | 0.02% | T -> A |
mr1011 (All); LR P-value: 6.01E-06;
mr1138 (All); LR P-value: 3.49E-14; mr1138 (Ind_All); LR P-value: 4.27E-09; mr1193 (All); LR P-value: 2.15E-07; mr1518 (All); LR P-value: 1.02E-18; mr1637 (All); LR P-value: 4.23E-09; mr1707 (Ind_All); LR P-value: 1.73E-06; mr1728 (Ind_All); LR P-value: 2.19E-11; mr1860 (Ind_All); LR P-value: 9.43E-08; mr1138_2 (All); LR P-value: 2.17E-14; mr1138_2 (Ind_All); LR P-value: 3.99E-08; mr1707_2 (All); LMM P-value: 4.84E-06; mr1707_2 (Ind_All); LR P-value: 4.79E-06; mr1728_2 (All); LMM P-value: 3.09E-06; mr1728_2 (Ind_All); LR P-value: 1.05E-11; mr1860_2 (Ind_All); LR P-value: 5.85E-08 |
LOC_Os09g29930.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g29930.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 99.709; most accessible tissue: Zhenshan97 panicle, score: 99.894 |
| vg0918209558 (J) | chr09 | 18209558 | A | G | 55.70% | 0.04% | G -> A |
mr1011 (All); LR P-value: 9.25E-06;
mr1138 (All); LR P-value: 1.59E-13; mr1138 (Ind_All); LR P-value: 4.27E-09; mr1193 (All); LR P-value: 2.09E-07; mr1291 (All); LR P-value: 4.15E-06; mr1637 (All); LR P-value: 9.37E-09; mr1707 (Ind_All); LR P-value: 1.73E-06; mr1728 (Ind_All); LR P-value: 2.19E-11; mr1860 (Ind_All); LR P-value: 9.43E-08; mr1138_2 (All); LR P-value: 6.10E-14; mr1138_2 (Ind_All); LR P-value: 3.99E-08; mr1636_2 (All); LR P-value: 1.32E-11; mr1707_2 (Ind_All); LR P-value: 4.79E-06; mr1728_2 (All); LMM P-value: 1.62E-06; mr1728_2 (Ind_All); LR P-value: 1.05E-11; mr1860_2 (Ind_All); LR P-value: 5.85E-08 |
LOC_Os09g29930.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g29930.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 99.640; most accessible tissue: Zhenshan97 panicle, score: 99.855 |
| vg0918209596 (J) | chr09 | 18209596 | T | C | 55.70% | 0.04% | C -> T |
mr1011 (All); LR P-value: 9.25E-06;
mr1138 (All); LR P-value: 1.59E-13; mr1138 (Ind_All); LR P-value: 4.27E-09; mr1193 (All); LR P-value: 2.09E-07; mr1291 (All); LR P-value: 4.15E-06; mr1637 (All); LR P-value: 9.37E-09; mr1707 (Ind_All); LR P-value: 1.73E-06; mr1728 (Ind_All); LR P-value: 2.19E-11; mr1860 (Ind_All); LR P-value: 9.43E-08; mr1138_2 (All); LR P-value: 6.10E-14; mr1138_2 (Ind_All); LR P-value: 3.99E-08; mr1636_2 (All); LR P-value: 1.32E-11; mr1707_2 (Ind_All); LR P-value: 4.79E-06; mr1728_2 (All); LMM P-value: 1.62E-06; mr1728_2 (Ind_All); LR P-value: 1.05E-11; mr1860_2 (Ind_All); LR P-value: 5.85E-08 |
LOC_Os09g29930.2 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g29930.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os09g29930.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os09g29930.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os09g29930.3 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os09g29930.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 98.233; most accessible tissue: Zhenshan97 panicle, score: 99.724 |
| vg0918209818 (J) | chr09 | 18209818 | G | A | 55.80% | 0.04% | A -> G |
mr1011 (All); LR P-value: 8.53E-06;
mr1138 (All); LR P-value: 2.45E-14; mr1138 (Ind_All); LR P-value: 3.08E-09; mr1193 (All); LR P-value: 1.53E-07; mr1291 (All); LR P-value: 2.40E-06; mr1518 (All); LR P-value: 9.24E-20; mr1518 (Ind_All); LR P-value: 1.93E-06; mr1637 (All); LR P-value: 3.78E-09; mr1676 (All); LR P-value: 4.57E-20; mr1676 (Ind_All); LR P-value: 4.13E-06; mr1693 (All); LR P-value: 8.77E-09; mr1707 (Ind_All); LR P-value: 1.35E-06; mr1728 (Ind_All); LR P-value: 9.47E-12; mr1860 (Ind_All); LR P-value: 1.82E-07; mr1138_2 (All); LR P-value: 9.95E-15; mr1138_2 (Ind_All); LR P-value: 2.12E-08; mr1369_2 (All); LR P-value: 2.20E-06; mr1636_2 (All); LR P-value: 1.37E-11; mr1691_2 (All); LR P-value: 2.28E-06; mr1707_2 (All); LMM P-value: 7.42E-06; mr1707_2 (Ind_All); LR P-value: 3.43E-06; mr1728_2 (All); LMM P-value: 3.44E-07; mr1728_2 (Ind_All); LMM P-value: 3.59E-06; LR P-value: 1.65E-12; mr1860_2 (Ind_All); LR P-value: 2.55E-08 |
LOC_Os09g29930.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g29930.3 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 96.604; most accessible tissue: Minghui63 flower, score: 98.948 |
| vg0918210148 (J) | chr09 | 18210148 | G | T | 89.90% | 0.23% | G -> T |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g29930.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.3 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g29930.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.431; most accessible tissue: Minghui63 flower, score: 98.212 |
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