40 variations found. Os09g0245500/LOC_Os09g07020 (oxidoreductase; putative; expressed), ranging from 3,404,353 bp to 3,408,176 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os09g07020 | oxidoreductase, putative, expressed; RAP ID: Os09g0245500; MSU ID: LOC_Os09g07020 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0903404722 (J) | chr09 | 3404722 | C | G | 62.10% | 0.02% | G -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os09g07010.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.790; most accessible tissue: Callus, score: 87.271 |
|
| vg0903405138 (J) | chr09 | 3405138 | T | C | 54.60% | 0.00% | C -> T |
LOC_Os09g07010.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.339; most accessible tissue: Zhenshan97 root, score: 79.710 |
|
| vg0903405165 (J) | chr09 | 3405165 | A | T | 99.20% | 0.00% | A -> T | NA |
LOC_Os09g07010.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.352; most accessible tissue: Zhenshan97 root, score: 77.733 |
| vg0903405239 (J) | chr09 | 3405239 | A | T | 99.60% | 0.00% | A -> T | NA |
LOC_Os09g07010.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.837; most accessible tissue: Callus, score: 84.863 |
| vg0903405351 (J) | chr09 | 3405351 | G | A | 86.70% | 0.00% | G -> A |
Grain_thickness (Jap_All); LR P-value: 2.28E-14;
mr1206 (All); LR P-value: 1.36E-06; mr1301 (Jap_All); LR P-value: 5.80E-14; mr1554 (All); LR P-value: 5.56E-07; mr1596 (All); LR P-value: 3.03E-07; mr1880 (All); LR P-value: 1.32E-06; mr1916 (Jap_All); LR P-value: 2.84E-08; mr1993 (Jap_All); LR P-value: 6.56E-08; mr1184_2 (All); LR P-value: 4.70E-06; mr1277_2 (Jap_All); LR P-value: 1.19E-06; mr1363_2 (Jap_All); LR P-value: 4.48E-06; mr1488_2 (All); LR P-value: 2.31E-06; mr1502_2 (All); LR P-value: 2.32E-07; mr1552_2 (All); LR P-value: 1.23E-13; mr1552_2 (Jap_All); LR P-value: 1.10E-10; mr1554_2 (All); LR P-value: 6.82E-08; mr1556_2 (All); LR P-value: 5.20E-06; mr1578_2 (Jap_All); LR P-value: 2.73E-09; mr1593_2 (All); LR P-value: 2.54E-13; mr1786_2 (All); LR P-value: 9.81E-06; mr1812_2 (All); LR P-value: 5.46E-06; mr1864_2 (All); LR P-value: 2.03E-14; mr1864_2 (Jap_All); LR P-value: 2.37E-09; mr1980_2 (Jap_All); LR P-value: 5.39E-06 |
LOC_Os09g07010.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.744; most accessible tissue: Zhenshan97 root, score: 73.600 |
| vg0903405622 (J) | chr09 | 3405622 | A | C | 99.30% | 0.00% | A -> C | NA |
LOC_Os09g07010.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.936; most accessible tissue: Zhenshan97 root, score: 65.566 |
| vg0903405692 (J) | chr09 | 3405692 | TA | T | 92.50% | 0.00% | TA -> T | NA |
LOC_Os09g07010.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.859; most accessible tissue: Callus, score: 77.599 |
| vg0903405748 (J) | chr09 | 3405748 | A | T | 63.90% | 0.00% | T -> A | NA |
LOC_Os09g07010.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.330; most accessible tissue: Callus, score: 77.599 |
| vg0903405841 (J) | chr09 | 3405841 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os09g07010.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.340; most accessible tissue: Zhenshan97 young leaf, score: 74.302 |
| vg0903405844 (J) | chr09 | 3405844 | T | C | 99.20% | 0.00% | T -> C | NA |
LOC_Os09g07010.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.613; most accessible tissue: Zhenshan97 young leaf, score: 74.675 |
| vg0903405991 (J) | chr09 | 3405991 | A | G | 63.00% | 0.00% | G -> A | NA |
LOC_Os09g07020.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os09g07020.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 52.962; most accessible tissue: Zhenshan97 young leaf, score: 75.751 |
| vg0903406052 (J) | chr09 | 3406052 | G | A | 98.90% | 0.00% | G -> A | NA |
LOC_Os09g07020.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os09g07020.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 50.656; most accessible tissue: Zhenshan97 young leaf, score: 72.340 |
| vg0903406122 (J) | chr09 | 3406122 | C | T | 63.90% | 0.00% | T -> C | NA |
LOC_Os09g07010.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.456; most accessible tissue: Zhenshan97 young leaf, score: 65.280 |
| vg0903406215 (J) | chr09 | 3406215 | A | C | 86.60% | 0.00% | A -> C |
Grain_thickness (Jap_All); LR P-value: 2.28E-14;
mr1206 (All); LR P-value: 7.61E-07; mr1301 (Jap_All); LR P-value: 5.80E-14; mr1554 (All); LR P-value: 4.53E-07; mr1596 (All); LR P-value: 1.65E-07; mr1775 (All); LR P-value: 1.14E-10; mr1880 (All); LR P-value: 9.17E-07; mr1916 (Jap_All); LR P-value: 2.84E-08; mr1993 (Jap_All); LR P-value: 6.56E-08; mr1184_2 (All); LR P-value: 7.27E-06; mr1277_2 (Jap_All); LR P-value: 1.19E-06; mr1363_2 (Jap_All); LR P-value: 4.48E-06; mr1552_2 (All); LR P-value: 1.22E-13; mr1552_2 (Jap_All); LR P-value: 1.10E-10; mr1554_2 (All); LR P-value: 6.76E-08; mr1556_2 (All); LR P-value: 7.88E-06; mr1578_2 (Jap_All); LR P-value: 2.73E-09; mr1593_2 (All); LR P-value: 2.24E-12; mr1812_2 (All); LR P-value: 9.90E-06; mr1864_2 (All); LR P-value: 1.00E-13; mr1864_2 (Jap_All); LR P-value: 2.37E-09; mr1980_2 (Jap_All); LR P-value: 5.39E-06 |
LOC_Os09g07020.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os09g07020.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 47.836; most accessible tissue: Callus, score: 75.989 |
| vg0903406372 (J) | chr09 | 3406372 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os09g07010.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 42.056; most accessible tissue: Callus, score: 57.883 |
| vg0903406470 (J) | chr09 | 3406470 | C | T | 99.20% | 0.00% | C -> T | NA |
LOC_Os09g07010.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 43.405; most accessible tissue: Callus, score: 76.680 |
| vg0903406555 (J) | chr09 | 3406555 | A | C | 99.20% | 0.00% | A -> C | NA |
LOC_Os09g07010.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 47.342; most accessible tissue: Callus, score: 76.680 |
| vg0903406707 (J) | chr09 | 3406707 | CA | C | 99.30% | 0.00% | CA -> C,GA | NA |
LOC_Os09g07010.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)
LOC_Os09g07030.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff) LOC_Os09g07020.1 Alt: GA| intron_variant MODIFIER(snpEff) LOC_Os09g07020.2 Alt: GA| intron_variant MODIFIER(snpEff) LOC_Os09g07010.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.907; most accessible tissue: Callus, score: 78.358 |
| vg0903406771 (J) | chr09 | 3406771 | T | G | 99.80% | 0.00% | T -> G | NA |
LOC_Os09g07020.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os09g07020.2 Alt: G| synonymous_variant LOW(snpEff) LOC_Os09g07010.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os09g07030.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 52.894; most accessible tissue: Callus, score: 78.358 |
| vg0903406850 (J) | chr09 | 3406850 | T | G | 62.90% | 0.00% | G -> T | NA |
LOC_Os09g07010.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.109; most accessible tissue: Zhenshan97 young leaf, score: 70.177 |
| vg0903406892 (J) | chr09 | 3406892 | A | G | 99.60% | 0.00% | A -> G | NA |
LOC_Os09g07010.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.454; most accessible tissue: Zhenshan97 young leaf, score: 70.177 |
| vg0903407050 (J) | chr09 | 3407050 | G | T | 99.60% | 0.00% | G -> T | NA |
LOC_Os09g07010.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.195; most accessible tissue: Callus, score: 85.420 |
| vg0903407270 (J) | chr09 | 3407270 | T | C | 62.90% | 0.00% | C -> T |
LOC_Os09g07010.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07030.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 71.432; most accessible tissue: Callus, score: 81.654 |
|
| vg0903407290 (J) | chr09 | 3407290 | T | C | 99.20% | 0.00% | T -> C | NA |
LOC_Os09g07010.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os09g07040.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07030.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os09g07020.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.239; most accessible tissue: Callus, score: 81.654 |
| vg0903407426 (J) | chr09 | 3407426 | C | A | 86.70% | 0.00% | C -> A |
Grain_thickness (Jap_All); LR P-value: 3.30E-14;
mr1206 (All); LR P-value: 1.34E-06; mr1596 (All); LR P-value: 1.89E-07; mr1880 (All); LR P-value: 8.77E-07; mr1916 (Jap_All); LR P-value: 8.71E-08; mr1184_2 (All); LR P-value: 5.17E-06; mr1278_2 (All); LR P-value: 9.45E-06; mr1335_2 (All); LR P-value: 1.09E-07; mr1346_2 (Jap_All); LR P-value: 4.15E-06; mr1363_2 (Jap_All); LR P-value: 3.04E-06; mr1488_2 (All); LR P-value: 1.63E-06; mr1502_2 (All); LR P-value: 7.62E-08; mr1552_2 (All); LR P-value: 2.00E-13; mr1552_2 (Jap_All); LR P-value: 1.73E-10; mr1554_2 (All); LR P-value: 1.64E-07; mr1556_2 (All); LR P-value: 2.81E-06; mr1578_2 (Jap_All); LR P-value: 1.91E-08; mr1593_2 (All); LR P-value: 4.09E-13; mr1764_2 (All); LR P-value: 9.07E-06; mr1786_2 (All); LR P-value: 9.84E-06; mr1812_2 (All); LR P-value: 4.13E-06; mr1864_2 (All); LR P-value: 1.04E-13 |
LOC_Os09g07020.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os09g07020.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 76.813; most accessible tissue: Zhenshan97 flower, score: 86.908 |
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