39 variations found. LOC_Os07g18600 (OsFBL37 - F-box domain and LRR containing protein; expressed), ranging from 10,993,118 bp to 10,994,274 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0710993130 (J) | chr07 | 10993130 | A | AAT | 90.50% | 0.00% | A -> AAT | NA |
LOC_Os07g18600.1 Alt: AAT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 40.102; most accessible tissue: Callus, score: 67.589 |
| vg0710993147 (J) | chr07 | 10993147 | G | T | 90.50% | 0.00% | G -> T |
Awn_length (All); LR P-value: 8.09E-26;
mr1624 (Jap_All); LR P-value: 2.02E-09; mr1624_2 (Jap_All); LR P-value: 9.08E-09; mr1741_2 (Jap_All); LR P-value: 2.33E-06; mr1887_2 (Jap_All); LR P-value: 5.73E-06 |
LOC_Os07g18600.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 44.468; most accessible tissue: Zhenshan97 young leaf, score: 70.625 |
| vg0710993152 (J) | chr07 | 10993152 | A | T | 99.70% | 0.00% | A -> T | NA |
LOC_Os07g18600.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os07g18580.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g18610.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g18590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 44.944; most accessible tissue: Zhenshan97 young leaf, score: 71.497 |
| vg0710993154 (J) | chr07 | 10993154 | C | A | 99.70% | 0.00% | C -> A | NA |
LOC_Os07g18600.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g18580.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g18610.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g18590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 44.944; most accessible tissue: Zhenshan97 young leaf, score: 71.497 |
| vg0710993160 (J) | chr07 | 10993160 | T | C | 52.70% | 0.00% | C -> T | NA |
LOC_Os07g18600.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 45.145; most accessible tissue: Zhenshan97 young leaf, score: 71.497 |
| vg0710993182 (J) | chr07 | 10993182 | G | A | 90.60% | 0.00% | G -> A |
Awn_length (All); LR P-value: 9.39E-24;
mr1624 (Jap_All); LR P-value: 2.02E-09; mr1624_2 (Jap_All); LR P-value: 9.08E-09; mr1741_2 (Jap_All); LR P-value: 2.33E-06; mr1887_2 (Jap_All); LR P-value: 5.73E-06 |
LOC_Os07g18600.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 47.681; most accessible tissue: Callus, score: 88.323 |
| vg0710993290 (J) | chr07 | 10993290 | T | A | 97.60% | 0.00% | T -> A | NA |
LOC_Os07g18580.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g18610.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g18590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g18600.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.785; most accessible tissue: Callus, score: 88.323 |
| vg0710993311 (J) | chr07 | 10993311 | C | A | 98.30% | 0.00% | C -> A | NA |
LOC_Os07g18580.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g18610.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g18590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g18600.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.299; most accessible tissue: Callus, score: 88.323 |
| vg0710993360 (J) | chr07 | 10993360 | C | T | 63.60% | 0.00% | T -> C |
mr1075 (All); LR P-value: 1.79E-29;
mr1124 (All); LR P-value: 3.71E-40; mr1202 (All); LR P-value: 3.30E-29; mr1592 (All); LR P-value: 4.15E-14; mr1594 (All); LR P-value: 1.01E-58; mr1595 (All); LR P-value: 2.62E-08; mr1630 (All); LR P-value: 2.97E-10; mr1689 (All); LR P-value: 3.04E-21; mr1861 (All); LR P-value: 2.28E-54; mr1888 (All); LR P-value: 2.65E-25; mr1891 (All); LR P-value: 2.53E-40; mr1962 (All); LR P-value: 3.49E-60; mr1067_2 (All); LR P-value: 1.10E-55; mr1222_2 (All); LR P-value: 4.54E-09; mr1595_2 (All); LR P-value: 9.75E-11; mr1723_2 (All); LR P-value: 7.67E-34; mr1888_2 (All); LR P-value: 1.06E-34 |
LOC_Os07g18600.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 65.410; most accessible tissue: Zhenshan97 young leaf, score: 84.035 |
| vg0710993399 (J) | chr07 | 10993399 | G | A | 90.60% | 0.00% | G -> A |
Awn_length (All); LR P-value: 1.73E-26;
Awn_length (Jap_All); LR P-value: 7.72E-08; mr1624 (Jap_All); LR P-value: 4.60E-09; mr1624_2 (Jap_All); LR P-value: 2.89E-08; mr1741_2 (Jap_All); LR P-value: 5.57E-06 |
LOC_Os07g18600.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 64.176; most accessible tissue: Zhenshan97 young leaf, score: 82.982 |
| vg0710993519 (J) | chr07 | 10993519 | G | A | 98.30% | 0.00% | G -> A | NA |
LOC_Os07g18600.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.690; most accessible tissue: Zhenshan97 young leaf, score: 89.226 |
| vg0710993524 (J) | chr07 | 10993524 | A | G | 97.20% | 0.00% | A -> G | NA |
LOC_Os07g18600.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 74.737; most accessible tissue: Zhenshan97 young leaf, score: 89.112 |
| vg0710993606 (J) | chr07 | 10993606 | C | G | 90.60% | 0.00% | C -> G |
Awn_length (All); LR P-value: 8.09E-26;
mr1624 (Jap_All); LR P-value: 2.02E-09; mr1624_2 (Jap_All); LR P-value: 9.08E-09; mr1741_2 (Jap_All); LR P-value: 2.33E-06; mr1887_2 (Jap_All); LR P-value: 5.73E-06 |
LOC_Os07g18600.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 75.362; most accessible tissue: Zhenshan97 young leaf, score: 89.559 |
| vg0710993633 (J) | chr07 | 10993633 | G | T | 97.20% | 0.00% | G -> T | NA |
LOC_Os07g18600.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.783; most accessible tissue: Zhenshan97 young leaf, score: 89.339 |
| vg0710993640 (J) | chr07 | 10993640 | A | C | 98.30% | 0.00% | A -> C | NA |
LOC_Os07g18600.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 74.386; most accessible tissue: Zhenshan97 young leaf, score: 88.995 |
| vg0710993702 (J) | chr07 | 10993702 | C | CGCGGCG | 90.80% | 0.00% | C -> CGCGGCG | NA |
LOC_Os07g18600.1 Alt: CGCGGCG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 79.012; most accessible tissue: Zhenshan97 young leaf, score: 88.995 |
| vg0710993818 (J) | chr07 | 10993818 | C | T | 75.00% | 0.00% | T -> C |
Awn_length (Jap_All); LR P-value: 1.53E-07;
mr1578 (All); LR P-value: 3.07E-09; mr1677 (All); LR P-value: 2.94E-06; mr1900 (All); LR P-value: 2.88E-15; mr1905 (All); LR P-value: 4.89E-10; mr1042_2 (All); LR P-value: 1.56E-23; mr1062_2 (All); LR P-value: 7.21E-19; mr1167_2 (All); LR P-value: 1.62E-20; mr1167_2 (Jap_All); LR P-value: 7.10E-06; mr1227_2 (All); LR P-value: 1.58E-06; mr1405_2 (All); LR P-value: 2.11E-06; mr1479_2 (All); LR P-value: 6.17E-07; mr1574_2 (All); LR P-value: 8.67E-06; mr1624_2 (Jap_All); LR P-value: 2.43E-07; mr1636_2 (All); LR P-value: 1.88E-12; mr1641_2 (All); LR P-value: 4.62E-12; mr1646_2 (All); LR P-value: 4.24E-10; mr1681_2 (All); LR P-value: 1.16E-07; mr1717_2 (All); LR P-value: 4.60E-13; mr1726_2 (All); LR P-value: 1.20E-17; mr1726_2 (Jap_All); LR P-value: 8.07E-06; mr1741_2 (Jap_All); LR P-value: 8.32E-06; mr1765_2 (All); LR P-value: 3.09E-09; mr1838_2 (All); LR P-value: 3.59E-13 |
LOC_Os07g18600.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 79.919; most accessible tissue: Zhenshan97 young leaf, score: 87.859 |
| vg0710993846 (J) | chr07 | 10993846 | G | T | 51.80% | 0.00% | G -> T |
LOC_Os07g18600.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.350; most accessible tissue: Zhenshan97 young leaf, score: 86.383 |
|
| vg0710993848 (J) | chr07 | 10993848 | T | G | 90.50% | 0.00% | T -> G |
Awn_length (All); LR P-value: 8.09E-26;
mr1624 (Jap_All); LR P-value: 2.02E-09; mr1624_2 (Jap_All); LR P-value: 9.08E-09; mr1741_2 (Jap_All); LR P-value: 2.33E-06; mr1887_2 (Jap_All); LR P-value: 5.73E-06 |
LOC_Os07g18600.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.308; most accessible tissue: Zhenshan97 young leaf, score: 86.383 |
| vg0710993894 (J) | chr07 | 10993894 | G | A | 90.60% | 0.00% | G -> A |
Awn_length (All); LR P-value: 4.46E-27;
mr1624 (Jap_All); LR P-value: 2.02E-09; mr1624_2 (Jap_All); LR P-value: 9.08E-09; mr1741_2 (Jap_All); LR P-value: 2.33E-06; mr1887_2 (Jap_All); LR P-value: 5.73E-06 |
LOC_Os07g18600.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.608; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 |
| vg0710993896 (J) | chr07 | 10993896 | A | G | 90.60% | 0.00% | A -> G |
Awn_length (All); LR P-value: 8.09E-26;
mr1624 (Jap_All); LR P-value: 2.02E-09; mr1624_2 (Jap_All); LR P-value: 9.08E-09; mr1741_2 (Jap_All); LR P-value: 2.33E-06; mr1887_2 (Jap_All); LR P-value: 5.73E-06 |
LOC_Os07g18600.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.806; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 |
| vg0710993899 (J) | chr07 | 10993899 | A | G | 98.30% | 0.00% | A -> G | NA |
LOC_Os07g18600.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 77.104; most accessible tissue: Zhenshan97 flag leaf, score: 85.880 |
| vg0710993904 (J) | chr07 | 10993904 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os07g18600.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os07g18580.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g18610.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g18590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.103; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 |
| vg0710993935 (J) | chr07 | 10993935 | G | C | 75.00% | 0.00% | C -> G |
mr1238 (All); LR P-value: 6.99E-26;
mr1578 (All); LR P-value: 1.13E-09; mr1900 (All); LR P-value: 6.93E-16; mr1905 (All); LR P-value: 1.48E-10; mr1042_2 (All); LR P-value: 1.00E-23; mr1062_2 (All); LR P-value: 9.44E-19; mr1167_2 (All); LR P-value: 6.21E-20; mr1227_2 (All); LR P-value: 3.12E-06; mr1405_2 (All); LR P-value: 3.67E-06; mr1479_2 (All); LR P-value: 6.24E-07; mr1636_2 (All); LR P-value: 6.34E-12; mr1646_2 (All); LR P-value: 6.76E-10; mr1681_2 (All); LR P-value: 7.84E-08; mr1726_2 (All); LR P-value: 4.20E-17; mr1765_2 (All); LR P-value: 7.73E-09 |
LOC_Os07g18600.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 80.323; most accessible tissue: Minghui63 flag leaf, score: 86.766 |
| vg0710993983 (J) | chr07 | 10993983 | G | C | 98.40% | 0.00% | G -> C | NA |
LOC_Os07g18600.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 79.470; most accessible tissue: Minghui63 flag leaf, score: 88.103 |
| vg0710994016 (J) | chr07 | 10994016 | T | C | 52.70% | 0.00% | C -> T |
LOC_Os07g18600.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 79.405; most accessible tissue: Minghui63 flag leaf, score: 87.725 |
|
| vg0710994018 (J) | chr07 | 10994018 | T | A | 90.60% | 0.00% | T -> A |
Awn_length (All); LR P-value: 8.09E-26;
mr1624 (Jap_All); LR P-value: 2.02E-09; mr1624_2 (Jap_All); LR P-value: 9.08E-09; mr1741_2 (Jap_All); LR P-value: 2.33E-06; mr1887_2 (Jap_All); LR P-value: 5.73E-06 |
LOC_Os07g18600.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 79.405; most accessible tissue: Minghui63 flag leaf, score: 87.725 |
| vg0710994030 (J) | chr07 | 10994030 | C | G | 90.60% | 0.00% | C -> G |
Awn_length (All); LR P-value: 8.09E-26;
mr1624 (Jap_All); LR P-value: 2.02E-09; mr1624_2 (Jap_All); LR P-value: 9.08E-09; mr1741_2 (Jap_All); LR P-value: 2.33E-06; mr1887_2 (Jap_All); LR P-value: 5.73E-06 |
LOC_Os07g18600.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 78.964; most accessible tissue: Minghui63 flag leaf, score: 87.189 |
| vg0710994064 (J) | chr07 | 10994064 | G | A | 75.10% | 0.00% | A -> G |
mr1578 (All); LR P-value: 2.14E-09;
mr1900 (All); LR P-value: 1.68E-15; mr1905 (All); LR P-value: 7.40E-10; mr1042_2 (All); LR P-value: 1.07E-22; mr1062_2 (All); LR P-value: 1.09E-19; mr1167_2 (All); LR P-value: 1.15E-18; mr1227_2 (All); LR P-value: 1.01E-06; mr1405_2 (All); LR P-value: 2.06E-06; mr1574_2 (All); LR P-value: 4.64E-06; mr1636_2 (All); LR P-value: 1.14E-11; mr1641_2 (All); LR P-value: 9.28E-12; mr1646_2 (All); LR P-value: 5.24E-10; mr1726_2 (All); LR P-value: 3.79E-16; mr1751_2 (All); LR P-value: 1.36E-08; mr1761_2 (All); LR P-value: 1.10E-09; mr1765_2 (All); LR P-value: 5.92E-09 |
LOC_Os07g18600.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 77.091; most accessible tissue: Minghui63 flag leaf, score: 86.000 |
| vg0710994075 (J) | chr07 | 10994075 | C | A | 95.30% | 0.00% | C -> A |
Awn_length (Jap_All); LR P-value: 6.29E-08;
mr1624 (All); LR P-value: 1.08E-11; mr1624 (Jap_All); LR P-value: 2.59E-09; mr1057_2 (All); LR P-value: 4.39E-07; mr1624_2 (All); LR P-value: 6.52E-10; mr1624_2 (Jap_All); LR P-value: 1.42E-07; mr1741_2 (All); LR P-value: 1.16E-08; mr1757_2 (Jap_All); LR P-value: 6.21E-06 |
LOC_Os07g18600.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 77.499; most accessible tissue: Minghui63 flag leaf, score: 86.468 |
| vg0710994082 (J) | chr07 | 10994082 | G | A | 89.40% | 0.00% | G -> A | NA |
LOC_Os07g18600.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 75.444; most accessible tissue: Minghui63 flag leaf, score: 85.327 |
| vg0710994138 (J) | chr07 | 10994138 | C | G | 90.60% | 0.00% | C -> G |
Awn_length (All); LR P-value: 8.09E-26;
mr1624 (Jap_All); LR P-value: 2.02E-09; mr1624_2 (Jap_All); LR P-value: 9.08E-09; mr1741_2 (Jap_All); LR P-value: 2.33E-06; mr1887_2 (Jap_All); LR P-value: 5.73E-06 |
LOC_Os07g18600.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 74.542; most accessible tissue: Minghui63 flag leaf, score: 86.315 |
| vg0710994163 (J) | chr07 | 10994163 | C | G | 90.50% | 0.00% | C -> G |
Awn_length (All); LR P-value: 8.09E-26;
mr1624 (Jap_All); LR P-value: 2.02E-09; mr1624_2 (Jap_All); LR P-value: 9.08E-09; mr1741_2 (Jap_All); LR P-value: 2.33E-06; mr1887_2 (Jap_All); LR P-value: 5.73E-06 |
LOC_Os07g18600.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 73.775; most accessible tissue: Minghui63 flag leaf, score: 86.000 |
| vg0710994188 (J) | chr07 | 10994188 | A | G | 90.60% | 0.00% | A -> G |
Awn_length (All); LR P-value: 8.09E-26;
mr1624 (Jap_All); LR P-value: 2.02E-09; mr1624_2 (Jap_All); LR P-value: 9.08E-09; mr1741_2 (Jap_All); LR P-value: 2.33E-06; mr1887_2 (Jap_All); LR P-value: 5.73E-06 |
LOC_Os07g18600.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.579; most accessible tissue: Minghui63 flag leaf, score: 84.973 |
| vg0710994199 (J) | chr07 | 10994199 | C | CGCCAAG ATCGCT | 90.60% | 0.00% | C -> CGCCAAGATC GCT,T | NA |
LOC_Os07g18600.1 Alt: CGCCAAGATCGCT| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os07g18600.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 74.610; most accessible tissue: Minghui63 flag leaf, score: 85.327 |
| vg0710994221 (J) | chr07 | 10994221 | A | C | 90.60% | 0.00% | A -> C |
Awn_length (All); LR P-value: 8.09E-26;
mr1624 (Jap_All); LR P-value: 2.02E-09; mr1624_2 (Jap_All); LR P-value: 9.08E-09; mr1741_2 (Jap_All); LR P-value: 2.33E-06; mr1887_2 (Jap_All); LR P-value: 5.73E-06 |
LOC_Os07g18600.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 73.566; most accessible tissue: Minghui63 flag leaf, score: 86.315 |
| vg0710994234 (J) | chr07 | 10994234 | T | A | 99.90% | 0.00% | T -> A | NA |
LOC_Os07g18600.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g18580.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g18610.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g18590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 72.643; most accessible tissue: Minghui63 flag leaf, score: 85.500 |
| vg0710994254 (J) | chr07 | 10994254 | T | G | 90.60% | 0.00% | T -> G |
Awn_length (All); LR P-value: 1.73E-26;
Awn_length (Jap_All); LR P-value: 7.72E-08; mr1624 (Jap_All); LR P-value: 8.23E-10; mr1062_2 (Jap_All); LR P-value: 3.63E-06; mr1624_2 (Jap_All); LR P-value: 6.05E-09; mr1741_2 (Jap_All); LR P-value: 3.03E-06; mr1887_2 (Jap_All); LR P-value: 5.15E-06 |
LOC_Os07g18600.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.246; most accessible tissue: Minghui63 flag leaf, score: 87.052 |
| vg0710994274 (J) | chr07 | 10994274 | TGGCCGG CGGTA | T | 90.70% | 0.00% | TGGCCGGCGG TA -> T | NA |
LOC_Os07g18580.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g18600.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g18610.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g18590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g18600-LOC_Os07g18610 Alt: T| intergenic_region MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.312; most accessible tissue: Minghui63 flag leaf, score: 84.791 |