30 variations found. LOC_Os01g55630 (glutelin; putative; expressed), ranging from 32,052,965 bp to 32,054,348 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0132052984 (J) | chr01 | 32052984 | A | G | 75.90% | 0.00% | G -> A |
Grain_width (All); LR P-value: 3.21E-56;
mr1010 (All); LR P-value: 5.53E-14; mr1089 (All); LR P-value: 1.92E-42; mr1163 (All); LR P-value: 1.59E-22; mr1277 (All); LR P-value: 1.48E-10; mr1277 (Jap_All); LR P-value: 9.85E-06; mr1334 (All); LR P-value: 1.42E-87; mr1449 (Jap_All); LR P-value: 1.40E-08; mr1540 (Jap_All); LR P-value: 3.61E-15; mr1551 (Jap_All); LR P-value: 2.34E-07; mr1671 (Jap_All); LR P-value: 1.16E-06; mr1679 (All); LR P-value: 1.63E-20; mr1693 (All); LR P-value: 2.59E-09; mr1732 (Jap_All); LR P-value: 5.20E-16; mr1740 (All); LR P-value: 1.90E-15; mr1771 (All); LR P-value: 5.24E-48; mr1784 (All); LR P-value: 6.44E-37; mr1785 (All); LR P-value: 4.91E-07; mr1789 (All); LR P-value: 3.36E-29; mr1844 (All); LR P-value: 2.84E-13; mr1896 (Jap_All); LR P-value: 2.00E-06; mr1019_2 (All); LR P-value: 8.41E-71; mr1089_2 (All); LR P-value: 8.42E-52; mr1097_2 (Jap_All); LR P-value: 1.35E-06; mr1121_2 (Jap_All); LR P-value: 3.14E-06; mr1251_2 (All); LR P-value: 1.38E-36; mr1277_2 (All); LR P-value: 6.13E-15; mr1334_2 (All); LR P-value: 5.20E-101; mr1423_2 (All); LR P-value: 1.40E-28; mr1435_2 (All); LR P-value: 1.12E-36; mr1520_2 (All); LR P-value: 6.46E-12; mr1526_2 (Jap_All); LR P-value: 6.42E-08; mr1539_2 (Jap_All); LR P-value: 2.55E-14; mr1540_2 (Jap_All); LR P-value: 6.04E-15; mr1671_2 (Jap_All); LR P-value: 7.64E-07; mr1679_2 (All); LR P-value: 6.74E-21; mr1732_2 (Jap_All); LR P-value: 1.34E-13; mr1742_2 (Jap_All); LR P-value: 2.55E-09; mr1771_2 (All); LR P-value: 8.10E-41; mr1781_2 (Jap_All); LR P-value: 5.47E-06; mr1784_2 (All); LR P-value: 4.22E-44; mr1800_2 (All); LR P-value: 1.44E-13; mr1862_2 (All); LR P-value: 3.44E-39 |
LOC_Os01g55630.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 47.442; most accessible tissue: Callus, score: 71.356 |
| vg0132053002 (J) | chr01 | 32053002 | G | A | 96.80% | 0.00% | G -> A | NA |
LOC_Os01g55620.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 47.524; most accessible tissue: Callus, score: 71.356 |
| vg0132053026 (J) | chr01 | 32053026 | G | C | 76.00% | 0.00% | C -> G |
Grain_width (All); LR P-value: 3.20E-57;
mr1010 (All); LR P-value: 2.68E-14; mr1089 (All); LR P-value: 6.15E-44; mr1093 (All); LR P-value: 1.16E-41; mr1163 (All); LR P-value: 4.28E-23; mr1277 (All); LR P-value: 1.24E-10; mr1277 (Jap_All); LR P-value: 9.85E-06; mr1334 (All); LR P-value: 6.05E-86; mr1449 (Jap_All); LR P-value: 1.40E-08; mr1540 (Jap_All); LR P-value: 3.61E-15; mr1551 (Jap_All); LR P-value: 2.34E-07; mr1671 (Jap_All); LR P-value: 1.16E-06; mr1679 (All); LR P-value: 1.42E-20; mr1693 (All); LR P-value: 2.56E-09; mr1732 (Jap_All); LR P-value: 5.20E-16; mr1740 (All); LR P-value: 1.10E-15; mr1746 (All); LR P-value: 8.25E-09; mr1771 (All); LR P-value: 2.14E-47; mr1784 (All); LR P-value: 5.94E-37; mr1785 (All); LR P-value: 2.37E-07; mr1789 (All); LR P-value: 2.86E-29; mr1844 (All); LR P-value: 1.07E-13; mr1896 (Jap_All); LR P-value: 2.00E-06; mr1920 (All); LR P-value: 1.79E-21; mr1019_2 (All); LR P-value: 2.24E-71; mr1089_2 (All); LR P-value: 2.99E-53; mr1093_2 (All); LR P-value: 1.49E-49; mr1097_2 (Jap_All); LR P-value: 1.35E-06; mr1121_2 (Jap_All); LR P-value: 3.14E-06; mr1251_2 (All); LR P-value: 1.41E-37; mr1277_2 (All); LR P-value: 1.48E-14; mr1334_2 (All); LR P-value: 1.38E-99; mr1423_2 (All); LR P-value: 1.43E-29; mr1435_2 (All); LR P-value: 1.14E-37; mr1520_2 (All); LR P-value: 1.38E-11; mr1526_2 (Jap_All); LR P-value: 6.42E-08; mr1539_2 (Jap_All); LR P-value: 2.55E-14; mr1540_2 (Jap_All); LR P-value: 6.04E-15; mr1671_2 (Jap_All); LR P-value: 7.64E-07; mr1679_2 (All); LR P-value: 7.42E-21; mr1732_2 (Jap_All); LR P-value: 1.34E-13; mr1742_2 (Jap_All); LR P-value: 2.55E-09; mr1771_2 (All); LR P-value: 1.15E-40; mr1781_2 (Jap_All); LR P-value: 5.47E-06; mr1784_2 (All); LR P-value: 8.21E-44; mr1800_2 (All); LR P-value: 2.04E-13; mr1862_2 (All); LR P-value: 4.49E-39 |
LOC_Os01g55620.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.907; most accessible tissue: Callus, score: 71.356 |
| vg0132053054 (J) | chr01 | 32053054 | C | T | 86.10% | 0.00% | C -> T | NA |
LOC_Os01g55620.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 50.908; most accessible tissue: Callus, score: 71.356 |
| vg0132053134 (J) | chr01 | 32053134 | C | T | 79.20% | 0.00% | T -> C |
mr1010 (All); LR P-value: 4.24E-14;
mr1045 (All); LR P-value: 9.72E-08; mr1115 (All); LR P-value: 1.17E-22; mr1163 (All); LR P-value: 7.22E-24; mr1277 (All); LR P-value: 4.23E-10; mr1403 (Jap_All); LR P-value: 7.52E-07; mr1449 (Jap_All); LR P-value: 4.41E-09; mr1611 (All); LR P-value: 6.57E-23; mr1740 (All); LR P-value: 3.63E-13; mr1763 (All); LR P-value: 5.55E-07; mr1844 (All); LR P-value: 5.90E-15; mr1871 (Jap_All); LR P-value: 8.78E-06; mr1920 (All); LR P-value: 3.63E-24; mr1920 (Jap_All); LR P-value: 3.42E-12; mr1042_2 (Jap_All); LR P-value: 5.78E-09; mr1115_2 (All); LR P-value: 1.40E-24; mr1156_2 (All); LR P-value: 2.03E-18; mr1350_2 (Jap_All); LR P-value: 1.65E-07; mr1359_2 (Jap_All); LR P-value: 3.23E-06; mr1361_2 (All); LR P-value: 1.52E-20; mr1502_2 (Jap_All); LR P-value: 5.86E-08; mr1526_2 (Jap_All); LR P-value: 7.53E-08; mr1543_2 (Jap_All); LR P-value: 2.39E-10; mr1582_2 (Jap_All); LR P-value: 3.33E-06; mr1611_2 (All); LR P-value: 7.46E-22; mr1680_2 (Jap_All); LR P-value: 2.36E-07; mr1742_2 (Jap_All); LR P-value: 1.96E-11; mr1789_2 (Jap_All); LR P-value: 1.05E-11; mr1793_2 (Jap_All); LR P-value: 2.85E-07; mr1808_2 (Jap_All); LR P-value: 2.95E-07; mr1844_2 (All); LR P-value: 6.20E-12; mr1871_2 (Jap_All); LR P-value: 3.72E-11; mr1952_2 (Jap_All); LR P-value: 1.52E-08 |
LOC_Os01g55620.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.148; most accessible tissue: Minghui63 root, score: 60.831 |
| vg0132053221 (J) | chr01 | 32053221 | G | GAT | 79.20% | 0.00% | GAT -> G,GATAT | NA |
LOC_Os01g55630.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g55630.1 Alt: GATAT| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 45.083; most accessible tissue: Callus, score: 69.065 |
| vg0132053231 (J) | chr01 | 32053231 | C | T | 79.20% | 0.00% | T -> C |
mr1010 (All); LR P-value: 3.93E-14;
mr1045 (All); LR P-value: 9.04E-08; mr1163 (All); LR P-value: 2.68E-23; mr1277 (Jap_All); LR P-value: 9.89E-06; mr1403 (Jap_All); LR P-value: 7.00E-07; mr1449 (Jap_All); LR P-value: 1.29E-09; mr1543 (Jap_All); LR P-value: 1.76E-06; mr1551 (Jap_All); LR P-value: 4.14E-07; mr1671 (Jap_All); LR P-value: 1.70E-06; mr1723 (Jap_All); LR P-value: 4.88E-07; mr1740 (All); LR P-value: 7.23E-13; mr1789 (Jap_All); LR P-value: 3.06E-13; mr1844 (All); LR P-value: 2.47E-14; mr1871 (Jap_All); LR P-value: 2.81E-06; mr1896 (Jap_All); LR P-value: 4.61E-06; mr1920 (All); LR P-value: 1.38E-22; mr1920 (Jap_All); LR P-value: 4.93E-12; mr1010_2 (All); LR P-value: 4.43E-20; mr1042_2 (Jap_All); LR P-value: 3.73E-07; mr1089_2 (Jap_All); LR P-value: 1.78E-09; mr1156_2 (All); LR P-value: 8.00E-18; mr1334_2 (Jap_All); LR P-value: 2.15E-15; mr1359_2 (Jap_All); LR P-value: 9.54E-06; mr1526_2 (Jap_All); LR P-value: 1.06E-08; mr1539_2 (Jap_All); LR P-value: 7.18E-14; mr1540_2 (Jap_All); LR P-value: 6.56E-15; mr1543_2 (Jap_All); LR P-value: 2.58E-09; mr1671_2 (Jap_All); LR P-value: 1.15E-07; mr1730_2 (All); LR P-value: 1.83E-16; mr1732_2 (Jap_All); LR P-value: 1.64E-13; mr1742_2 (Jap_All); LR P-value: 2.40E-11; mr1784_2 (Jap_All); LR P-value: 3.61E-10; mr1789_2 (Jap_All); LR P-value: 9.53E-12; mr1793_2 (Jap_All); LR P-value: 5.77E-06; mr1844_2 (All); LR P-value: 3.26E-11; mr1871_2 (Jap_All); LR P-value: 6.92E-09 |
LOC_Os01g55630.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 44.632; most accessible tissue: Callus, score: 69.065 |
| vg0132053235 (J) | chr01 | 32053235 | A | T | 99.70% | 0.00% | A -> T | NA |
LOC_Os01g55630.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os01g55620.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g55640.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g55650.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 45.306; most accessible tissue: Callus, score: 69.065 |
| vg0132053349 (J) | chr01 | 32053349 | T | C | 75.90% | 0.00% | C -> T |
Grain_width (All); LR P-value: 3.04E-56;
mr1010 (All); LR P-value: 2.79E-13; mr1089 (All); LR P-value: 2.15E-42; mr1163 (All); LR P-value: 5.09E-21; mr1277 (All); LR P-value: 2.66E-10; mr1277 (Jap_All); LR P-value: 9.85E-06; mr1334 (All); LR P-value: 4.68E-85; mr1401 (All); LR P-value: 5.23E-15; mr1449 (Jap_All); LR P-value: 1.40E-08; mr1540 (Jap_All); LR P-value: 3.61E-15; mr1551 (Jap_All); LR P-value: 2.34E-07; mr1671 (Jap_All); LR P-value: 1.16E-06; mr1679 (All); LR P-value: 1.50E-20; mr1693 (All); LR P-value: 2.80E-09; mr1732 (Jap_All); LR P-value: 5.20E-16; mr1740 (All); LR P-value: 4.10E-15; mr1771 (All); LR P-value: 6.87E-46; mr1785 (All); LR P-value: 8.81E-07; mr1844 (All); LR P-value: 9.15E-13; mr1896 (Jap_All); LR P-value: 2.00E-06; mr1089_2 (All); LR P-value: 6.49E-53; mr1097_2 (Jap_All); LR P-value: 1.35E-06; mr1121_2 (Jap_All); LR P-value: 3.14E-06; mr1251_2 (All); LR P-value: 1.08E-36; mr1277_2 (All); LR P-value: 1.22E-14; mr1334_2 (All); LR P-value: 8.02E-98; mr1361_2 (All); LR P-value: 1.42E-20; mr1378_2 (All); LR P-value: 1.73E-08; mr1423_2 (All); LR P-value: 1.03E-28; mr1435_2 (All); LR P-value: 8.72E-37; mr1520_2 (All); LR P-value: 2.49E-12; mr1526_2 (Jap_All); LR P-value: 6.42E-08; mr1539_2 (Jap_All); LR P-value: 2.55E-14; mr1540_2 (Jap_All); LR P-value: 6.04E-15; mr1671_2 (Jap_All); LR P-value: 7.64E-07; mr1679_2 (All); LR P-value: 3.78E-21; mr1732_2 (Jap_All); LR P-value: 1.34E-13; mr1742_2 (Jap_All); LR P-value: 2.55E-09; mr1771_2 (All); LR P-value: 1.63E-39; mr1781_2 (Jap_All); LR P-value: 5.47E-06; mr1784_2 (All); LR P-value: 9.79E-43; mr1790_2 (All); LR P-value: 3.26E-14 |
LOC_Os01g55620.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 43.563; most accessible tissue: Zhenshan97 young leaf, score: 60.208 |
| vg0132053413 (J) | chr01 | 32053413 | C | T | 76.00% | 0.00% | T -> C |
Grain_width (All); LR P-value: 3.20E-57;
mr1010 (All); LR P-value: 2.68E-14; mr1089 (All); LR P-value: 6.15E-44; mr1093 (All); LR P-value: 1.16E-41; mr1163 (All); LR P-value: 4.28E-23; mr1277 (All); LR P-value: 1.24E-10; mr1277 (Jap_All); LR P-value: 9.85E-06; mr1334 (All); LR P-value: 6.05E-86; mr1449 (Jap_All); LR P-value: 1.40E-08; mr1540 (Jap_All); LR P-value: 3.61E-15; mr1551 (Jap_All); LR P-value: 2.34E-07; mr1671 (Jap_All); LR P-value: 1.16E-06; mr1679 (All); LR P-value: 1.42E-20; mr1693 (All); LR P-value: 2.56E-09; mr1732 (Jap_All); LR P-value: 5.20E-16; mr1740 (All); LR P-value: 1.10E-15; mr1746 (All); LR P-value: 8.25E-09; mr1771 (All); LR P-value: 2.14E-47; mr1784 (All); LR P-value: 5.94E-37; mr1785 (All); LR P-value: 2.37E-07; mr1789 (All); LR P-value: 2.86E-29; mr1844 (All); LR P-value: 1.07E-13; mr1896 (Jap_All); LR P-value: 2.00E-06; mr1920 (All); LR P-value: 1.79E-21; mr1019_2 (All); LR P-value: 2.24E-71; mr1089_2 (All); LR P-value: 2.99E-53; mr1093_2 (All); LR P-value: 1.49E-49; mr1097_2 (Jap_All); LR P-value: 1.35E-06; mr1121_2 (Jap_All); LR P-value: 3.14E-06; mr1251_2 (All); LR P-value: 1.41E-37; mr1277_2 (All); LR P-value: 1.48E-14; mr1334_2 (All); LR P-value: 1.38E-99; mr1423_2 (All); LR P-value: 1.43E-29; mr1435_2 (All); LR P-value: 1.14E-37; mr1520_2 (All); LR P-value: 1.38E-11; mr1526_2 (Jap_All); LR P-value: 6.42E-08; mr1539_2 (Jap_All); LR P-value: 2.55E-14; mr1540_2 (Jap_All); LR P-value: 6.04E-15; mr1671_2 (Jap_All); LR P-value: 7.64E-07; mr1679_2 (All); LR P-value: 7.42E-21; mr1732_2 (Jap_All); LR P-value: 1.34E-13; mr1742_2 (Jap_All); LR P-value: 2.55E-09; mr1771_2 (All); LR P-value: 1.15E-40; mr1781_2 (Jap_All); LR P-value: 5.47E-06; mr1784_2 (All); LR P-value: 8.21E-44; mr1800_2 (All); LR P-value: 2.04E-13; mr1862_2 (All); LR P-value: 4.49E-39 |
LOC_Os01g55620.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 39.674; most accessible tissue: Zhenshan97 young leaf, score: 59.009 |
| vg0132053733 (J) | chr01 | 32053733 | C | T | 76.00% | 0.00% | T -> C |
Grain_width (All); LR P-value: 4.56E-57;
mr1010 (All); LR P-value: 3.73E-14; mr1089 (All); LR P-value: 4.53E-43; mr1093 (All); LR P-value: 7.96E-41; mr1163 (All); LR P-value: 4.06E-23; mr1277 (All); LR P-value: 5.11E-10; mr1334 (All); LR P-value: 4.03E-85; mr1449 (Jap_All); LR P-value: 8.34E-09; mr1540 (Jap_All); LR P-value: 1.11E-14; mr1671 (Jap_All); LR P-value: 2.67E-06; mr1679 (All); LR P-value: 2.05E-20; mr1691 (All); LR P-value: 2.15E-08; mr1693 (All); LR P-value: 3.23E-09; mr1740 (All); LR P-value: 2.13E-15; mr1771 (All); LR P-value: 2.92E-46; mr1784 (All); LR P-value: 1.36E-36; mr1785 (All); LR P-value: 5.74E-07; mr1789 (All); LR P-value: 2.88E-29; mr1844 (All); LR P-value: 1.92E-13; mr1896 (Jap_All); LR P-value: 9.01E-06; mr1010_2 (All); LR P-value: 2.74E-20; mr1019_2 (All); LR P-value: 2.11E-69; mr1089_2 (All); LR P-value: 4.15E-53; mr1093_2 (All); LR P-value: 2.06E-49; mr1097_2 (Jap_All); LR P-value: 1.80E-06; mr1121_2 (Jap_All); LR P-value: 2.61E-06; mr1251_2 (All); LR P-value: 1.10E-37; mr1334_2 (All); LR P-value: 5.52E-98; mr1423_2 (All); LR P-value: 1.91E-29; mr1435_2 (All); LR P-value: 8.86E-38; mr1520_2 (All); LR P-value: 2.85E-11; mr1526_2 (Jap_All); LR P-value: 1.01E-08; mr1539_2 (Jap_All); LR P-value: 3.02E-14; mr1679_2 (All); LR P-value: 9.27E-21; mr1742_2 (Jap_All); LR P-value: 7.24E-10; mr1771_2 (All); LR P-value: 1.91E-40; mr1781_2 (Jap_All); LR P-value: 2.33E-06; mr1784_2 (All); LR P-value: 8.59E-44; mr1800_2 (All); LR P-value: 2.49E-13; mr1844_2 (All); LR P-value: 8.25E-11; mr1862_2 (All); LR P-value: 7.26E-39 |
LOC_Os01g55620.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 36.505; most accessible tissue: Callus, score: 74.920 |
| vg0132053749 (J) | chr01 | 32053749 | G | A | 79.10% | 0.00% | A -> G |
mr1010 (All); LR P-value: 3.40E-14;
mr1045 (All); LR P-value: 8.32E-08; mr1056 (All); LR P-value: 1.01E-12; mr1115 (All); LR P-value: 9.63E-23; mr1163 (All); LR P-value: 4.50E-24; mr1277 (All); LR P-value: 3.60E-10; mr1403 (Jap_All); LR P-value: 7.52E-07; mr1449 (Jap_All); LR P-value: 4.41E-09; mr1611 (All); LR P-value: 4.62E-23; mr1740 (All); LR P-value: 3.65E-13; mr1763 (All); LR P-value: 4.78E-07; mr1789 (All); LR P-value: 6.11E-29; mr1844 (All); LR P-value: 4.30E-15; mr1871 (Jap_All); LR P-value: 8.78E-06; mr1920 (All); LR P-value: 2.43E-24; mr1920 (Jap_All); LR P-value: 3.42E-12; mr1042_2 (Jap_All); LR P-value: 5.78E-09; mr1115_2 (All); LR P-value: 1.45E-24; mr1156_2 (All); LR P-value: 2.21E-18; mr1350_2 (Jap_All); LR P-value: 1.65E-07; mr1359_2 (Jap_All); LR P-value: 3.23E-06; mr1361_2 (All); LR P-value: 1.12E-20; mr1502_2 (Jap_All); LR P-value: 5.86E-08; mr1526_2 (Jap_All); LR P-value: 7.53E-08; mr1543_2 (Jap_All); LR P-value: 2.39E-10; mr1582_2 (Jap_All); LR P-value: 3.33E-06; mr1611_2 (All); LR P-value: 6.00E-22; mr1680_2 (Jap_All); LR P-value: 2.36E-07; mr1742_2 (Jap_All); LR P-value: 1.96E-11; mr1789_2 (Jap_All); LR P-value: 1.05E-11; mr1793_2 (Jap_All); LR P-value: 2.85E-07; mr1808_2 (Jap_All); LR P-value: 2.95E-07; mr1844_2 (All); LR P-value: 5.32E-12; mr1871_2 (Jap_All); LR P-value: 3.72E-11; mr1952_2 (Jap_All); LR P-value: 1.52E-08 |
LOC_Os01g55620.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.479; most accessible tissue: Callus, score: 74.920 |
| vg0132053752 (J) | chr01 | 32053752 | A | G | 75.90% | 0.00% | G -> A |
Grain_width (All); LR P-value: 2.67E-56;
mr1010 (All); LR P-value: 4.86E-14; mr1045 (All); LR P-value: 1.37E-07; mr1089 (All); LR P-value: 2.26E-42; mr1163 (All); LR P-value: 1.29E-22; mr1277 (All); LR P-value: 1.44E-10; mr1277 (Jap_All); LR P-value: 9.85E-06; mr1334 (All); LR P-value: 1.81E-87; mr1449 (Jap_All); LR P-value: 1.40E-08; mr1540 (Jap_All); LR P-value: 3.61E-15; mr1551 (Jap_All); LR P-value: 2.34E-07; mr1671 (Jap_All); LR P-value: 1.16E-06; mr1679 (All); LR P-value: 1.62E-20; mr1691 (All); LR P-value: 3.69E-08; mr1693 (All); LR P-value: 2.11E-09; mr1732 (Jap_All); LR P-value: 5.20E-16; mr1740 (All); LR P-value: 1.68E-15; mr1771 (All); LR P-value: 4.29E-48; mr1784 (All); LR P-value: 3.90E-37; mr1785 (All); LR P-value: 5.15E-07; mr1789 (All); LR P-value: 2.66E-29; mr1844 (All); LR P-value: 2.77E-13; mr1896 (Jap_All); LR P-value: 2.00E-06; mr1019_2 (All); LR P-value: 9.06E-71; mr1089_2 (All); LR P-value: 7.62E-52; mr1097_2 (Jap_All); LR P-value: 1.35E-06; mr1121_2 (Jap_All); LR P-value: 3.14E-06; mr1251_2 (All); LR P-value: 1.33E-36; mr1277_2 (All); LR P-value: 7.77E-15; mr1334_2 (All); LR P-value: 5.76E-101; mr1423_2 (All); LR P-value: 1.22E-28; mr1435_2 (All); LR P-value: 1.07E-36; mr1520_2 (All); LR P-value: 8.19E-12; mr1526_2 (Jap_All); LR P-value: 6.42E-08; mr1539_2 (Jap_All); LR P-value: 2.55E-14; mr1540_2 (Jap_All); LR P-value: 6.04E-15; mr1671_2 (Jap_All); LR P-value: 7.64E-07; mr1679_2 (All); LR P-value: 6.49E-21; mr1732_2 (Jap_All); LR P-value: 1.34E-13; mr1742_2 (Jap_All); LR P-value: 2.55E-09; mr1771_2 (All); LR P-value: 4.94E-41; mr1781_2 (Jap_All); LR P-value: 5.47E-06; mr1784_2 (All); LR P-value: 2.48E-44; mr1800_2 (All); LR P-value: 1.01E-13; mr1862_2 (All); LR P-value: 2.24E-39 |
LOC_Os01g55620.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.998; most accessible tissue: Callus, score: 74.920 |
| vg0132053764 (J) | chr01 | 32053764 | A | G | 97.90% | 0.00% | A -> G | NA |
LOC_Os01g55620.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.794; most accessible tissue: Callus, score: 74.920 |
| vg0132053806 (J) | chr01 | 32053806 | C | T | 97.90% | 0.00% | C -> T | NA |
LOC_Os01g55620.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 41.845; most accessible tissue: Callus, score: 74.920 |
| vg0132053807 (J) | chr01 | 32053807 | C | T | 97.90% | 0.00% | C -> T | NA |
LOC_Os01g55620.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 41.845; most accessible tissue: Callus, score: 74.920 |
| vg0132053833 (J) | chr01 | 32053833 | A | G | 52.30% | 0.00% | G -> A |
Grain_length (All); LR P-value: 1.21E-15;
mr1069 (Ind_All); LR P-value: 1.98E-06; mr1072 (Ind_All); LR P-value: 6.52E-06; mr1075 (Ind_All); LR P-value: 7.74E-07; mr1077 (Ind_All); LR P-value: 1.36E-06; mr1100 (Ind_All); LR P-value: 2.83E-06; mr1115 (Ind_All); LR P-value: 8.39E-06; mr1149 (Ind_All); LR P-value: 5.37E-07; mr1174 (All); LR P-value: 9.60E-09; mr1202 (Ind_All); LR P-value: 2.65E-06; mr1214 (Ind_All); LR P-value: 4.52E-06; mr1274 (Ind_All); LR P-value: 2.26E-06; mr1319 (Ind_All); LR P-value: 2.59E-06; mr1327 (Ind_All); LR P-value: 1.95E-06; mr1334 (Jap_All); LR P-value: 8.71E-14; mr1343 (Ind_All); LR P-value: 6.15E-07; mr1347 (All); LR P-value: 8.76E-06; mr1347 (Ind_All); LR P-value: 8.72E-06; mr1372 (Ind_All); LMM P-value: 6.93E-06; mr1427 (Ind_All); LMM P-value: 3.24E-06; mr1441 (Ind_All); LR P-value: 2.12E-08; mr1449 (Jap_All); LR P-value: 1.07E-08; mr1481 (Ind_All); LMM P-value: 2.30E-06; LR P-value: 2.30E-06; mr1540 (Jap_All); LR P-value: 3.20E-15; mr1594 (Ind_All); LMM P-value: 6.45E-06; mr1598 (Ind_All); LR P-value: 8.32E-06; mr1613 (Ind_All); LR P-value: 4.37E-07; mr1619 (Ind_All); LR P-value: 2.28E-06; mr1633 (Ind_All); LR P-value: 8.57E-06; mr1659 (Ind_All); LR P-value: 6.97E-06; mr1671 (Jap_All); LR P-value: 1.31E-06; mr1715 (Ind_All); LR P-value: 7.53E-06; mr1732 (Jap_All); LR P-value: 4.60E-16; mr1763 (Ind_All); LMM P-value: 3.74E-06; LR P-value: 1.61E-07; mr1839 (Ind_All); LR P-value: 5.87E-07; mr1896 (Jap_All); LR P-value: 6.04E-06; mr1901 (Ind_All); LR P-value: 6.84E-06; mr1909 (Ind_All); LR P-value: 2.21E-06; mr1921 (Ind_All); LR P-value: 8.24E-06; mr1962 (Ind_All); LR P-value: 6.13E-08; mr1097_2 (Jap_All); LR P-value: 1.06E-06; mr1121_2 (Jap_All); LR P-value: 2.49E-06; mr1128_2 (Ind_All); LR P-value: 6.52E-07; mr1174_2 (All); LR P-value: 6.68E-11; mr1274_2 (Ind_All); LR P-value: 1.57E-07; mr1327_2 (All); LR P-value: 1.40E-08; mr1334_2 (Jap_All); LR P-value: 7.09E-17; mr1347_2 (All); LR P-value: 1.53E-11; mr1364_2 (All); LR P-value: 6.35E-09; mr1425_2 (Jap_All); LR P-value: 8.20E-06; mr1441_2 (Ind_All); LR P-value: 3.98E-08; mr1471_2 (Jap_All); LR P-value: 9.38E-11; mr1480_2 (Ind_All); LR P-value: 9.95E-06; mr1526_2 (Jap_All); LR P-value: 3.40E-08; mr1539_2 (Jap_All); LR P-value: 4.29E-15; mr1540_2 (Jap_All); LR P-value: 4.15E-15; mr1619_2 (Ind_All); LR P-value: 1.56E-07; mr1671_2 (Jap_All); LR P-value: 7.24E-07; mr1699_2 (Jap_All); LR P-value: 1.62E-17; mr1732_2 (Jap_All); LR P-value: 1.05E-13; mr1742_2 (Jap_All); LR P-value: 2.95E-09; mr1771_2 (Jap_All); LR P-value: 9.92E-10; mr1781_2 (Jap_All); LR P-value: 4.18E-06; mr1784_2 (Jap_All); LR P-value: 1.43E-10; mr1795_2 (Ind_All); LR P-value: 3.84E-06; mr1798_2 (Jap_All); LR P-value: 1.51E-06; mr1817_2 (Jap_All); LR P-value: 9.35E-08; mr1862_2 (Jap_All); LR P-value: 7.85E-09; mr1962_2 (Ind_All); LR P-value: 9.38E-09; mr1991_2 (Jap_All); LR P-value: 2.29E-07; mr1993_2 (All); LR P-value: 1.82E-10 |
LOC_Os01g55620.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 40.003; most accessible tissue: Minghui63 panicle, score: 53.770 |
| vg0132053838 (J) | chr01 | 32053838 | G | T | 98.40% | 0.00% | G -> T | NA |
LOC_Os01g55620.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 40.393; most accessible tissue: Minghui63 panicle, score: 53.770 |
| vg0132053883 (J) | chr01 | 32053883 | A | G | 75.90% | 0.00% | G -> A |
Grain_width (All); LR P-value: 5.91E-57;
mr1010 (All); LR P-value: 2.54E-13; mr1089 (All); LR P-value: 7.07E-43; mr1093 (All); LR P-value: 2.26E-41; mr1163 (All); LR P-value: 2.62E-21; mr1277 (All); LR P-value: 1.80E-10; mr1277 (Jap_All); LR P-value: 9.85E-06; mr1334 (All); LR P-value: 4.02E-85; mr1401 (All); LR P-value: 3.51E-15; mr1449 (Jap_All); LR P-value: 1.40E-08; mr1540 (Jap_All); LR P-value: 3.61E-15; mr1551 (Jap_All); LR P-value: 2.34E-07; mr1671 (Jap_All); LR P-value: 1.16E-06; mr1679 (All); LR P-value: 1.39E-20; mr1691 (All); LR P-value: 2.09E-08; mr1693 (All); LR P-value: 1.99E-09; mr1732 (Jap_All); LR P-value: 5.20E-16; mr1740 (All); LR P-value: 3.71E-15; mr1771 (All); LR P-value: 7.56E-46; mr1785 (All); LR P-value: 8.01E-07; mr1844 (All); LR P-value: 1.43E-12; mr1896 (Jap_All); LR P-value: 2.00E-06; mr1920 (All); LR P-value: 1.43E-21; mr1089_2 (All); LR P-value: 5.93E-54; mr1093_2 (All); LR P-value: 9.58E-50; mr1097_2 (Jap_All); LR P-value: 1.35E-06; mr1121_2 (Jap_All); LR P-value: 3.14E-06; mr1156_2 (All); LR P-value: 3.58E-18; mr1248_2 (All); LR P-value: 1.70E-12; mr1251_2 (All); LR P-value: 1.17E-37; mr1277_2 (All); LR P-value: 7.35E-15; mr1334_2 (All); LR P-value: 3.86E-97; mr1378_2 (All); LR P-value: 1.80E-08; mr1423_2 (All); LR P-value: 6.92E-30; mr1435_2 (All); LR P-value: 9.43E-38; mr1520_2 (All); LR P-value: 3.27E-12; mr1526_2 (Jap_All); LR P-value: 6.42E-08; mr1539_2 (Jap_All); LR P-value: 2.55E-14; mr1540_2 (Jap_All); LR P-value: 6.04E-15; mr1671_2 (Jap_All); LR P-value: 7.64E-07; mr1679_2 (All); LR P-value: 1.10E-21; mr1732_2 (Jap_All); LR P-value: 1.34E-13; mr1742_2 (Jap_All); LR P-value: 2.55E-09; mr1771_2 (All); LR P-value: 2.45E-40; mr1781_2 (Jap_All); LR P-value: 5.47E-06; mr1784_2 (All); LR P-value: 8.50E-44; mr1790_2 (All); LR P-value: 1.37E-14; mr1800_2 (All); LR P-value: 9.75E-14; mr1844_2 (All); LR P-value: 4.49E-11; mr1862_2 (All); LR P-value: 1.57E-38 |
LOC_Os01g55620.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.926; most accessible tissue: Minghui63 panicle, score: 56.842 |
| vg0132053897 (J) | chr01 | 32053897 | TA | T | 60.10% | 0.00% | T -> TAA,TA,TAA A | NA |
LOC_Os01g55620.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g55640.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55620.1 Alt: TAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55640.1 Alt: TAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: TAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: TAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55620.1 Alt: TAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55640.1 Alt: TAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: TAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55630.1 Alt: TAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.552; most accessible tissue: Minghui63 panicle, score: 56.842 |
| vg0132054003 (J) | chr01 | 32054003 | G | A | 76.00% | 0.00% | A -> G |
Grain_width (All); LR P-value: 6.90E-57;
mr1010 (All); LR P-value: 3.38E-14; mr1089 (All); LR P-value: 1.12E-43; mr1093 (All); LR P-value: 3.21E-41; mr1163 (All); LR P-value: 6.97E-23; mr1277 (All); LR P-value: 1.48E-10; mr1277 (Jap_All); LR P-value: 9.85E-06; mr1334 (All); LR P-value: 9.30E-86; mr1449 (Jap_All); LR P-value: 1.40E-08; mr1540 (Jap_All); LR P-value: 3.61E-15; mr1551 (Jap_All); LR P-value: 2.34E-07; mr1671 (Jap_All); LR P-value: 1.16E-06; mr1679 (All); LR P-value: 1.65E-20; mr1693 (All); LR P-value: 2.49E-09; mr1732 (Jap_All); LR P-value: 5.20E-16; mr1740 (All); LR P-value: 1.09E-15; mr1771 (All); LR P-value: 3.65E-47; mr1784 (All); LR P-value: 8.55E-37; mr1785 (All); LR P-value: 2.75E-07; mr1789 (All); LR P-value: 2.98E-29; mr1844 (All); LR P-value: 1.47E-13; mr1896 (Jap_All); LR P-value: 2.00E-06; mr1019_2 (All); LR P-value: 4.83E-71; mr1089_2 (All); LR P-value: 4.79E-53; mr1093_2 (All); LR P-value: 3.88E-49; mr1097_2 (Jap_All); LR P-value: 1.35E-06; mr1121_2 (Jap_All); LR P-value: 3.14E-06; mr1251_2 (All); LR P-value: 2.63E-37; mr1277_2 (All); LR P-value: 1.45E-14; mr1334_2 (All); LR P-value: 4.52E-99; mr1423_2 (All); LR P-value: 2.80E-29; mr1435_2 (All); LR P-value: 2.13E-37; mr1520_2 (All); LR P-value: 9.93E-12; mr1526_2 (Jap_All); LR P-value: 6.42E-08; mr1539_2 (Jap_All); LR P-value: 2.55E-14; mr1540_2 (Jap_All); LR P-value: 6.04E-15; mr1671_2 (Jap_All); LR P-value: 7.64E-07; mr1679_2 (All); LR P-value: 7.78E-21; mr1732_2 (Jap_All); LR P-value: 1.34E-13; mr1742_2 (Jap_All); LR P-value: 2.55E-09; mr1771_2 (All); LR P-value: 1.72E-40; mr1781_2 (Jap_All); LR P-value: 5.47E-06; mr1784_2 (All); LR P-value: 1.38E-43; mr1800_2 (All); LR P-value: 1.81E-13; mr1862_2 (All); LR P-value: 8.91E-39 |
LOC_Os01g55630.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 42.693; most accessible tissue: Callus, score: 84.144 |
| vg0132054023 (J) | chr01 | 32054023 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os01g55630.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 43.748; most accessible tissue: Callus, score: 84.144 |
| vg0132054027 (J) | chr01 | 32054027 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os01g55630.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 43.701; most accessible tissue: Callus, score: 84.144 |
| vg0132054059 (J) | chr01 | 32054059 | G | A | 96.80% | 0.00% | G -> A | NA |
LOC_Os01g55630.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g55620.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55640.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 45.386; most accessible tissue: Callus, score: 84.144 |
| vg0132054062 (J) | chr01 | 32054062 | C | G | 99.00% | 0.00% | C -> G | NA |
LOC_Os01g55630.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g55620.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55640.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g55650.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 45.497; most accessible tissue: Callus, score: 84.144 |
| vg0132054282 (J) | chr01 | 32054282 | G | A | 61.60% | 0.00% | G -> A |
Grain_length (All); LR P-value: 1.29E-14;
Plant_height (Ind_All); LR P-value: 2.21E-15; mr1319 (Ind_All); LR P-value: 6.74E-06; mr1352 (Ind_All); LR P-value: 4.73E-06; mr1540 (Jap_All); LR P-value: 5.03E-14; mr1633 (Ind_All); LR P-value: 1.75E-06; mr1671 (Jap_All); LR P-value: 1.44E-06; mr1742 (All); LR P-value: 4.68E-06; mr1896 (Jap_All); LR P-value: 6.08E-06; mr1045_2 (Ind_All); LR P-value: 1.25E-06; mr1115_2 (Ind_All); LR P-value: 2.93E-06; mr1174_2 (All); LR P-value: 2.31E-11; mr1268_2 (All); LR P-value: 2.93E-07; mr1268_2 (Ind_All); LR P-value: 2.54E-06; mr1277_2 (Ind_All); LR P-value: 1.77E-06; mr1319_2 (Ind_All); LR P-value: 1.66E-06; mr1327_2 (All); LR P-value: 1.95E-14; mr1327_2 (Ind_All); LR P-value: 3.10E-12; mr1330_2 (Ind_All); LR P-value: 2.30E-07; mr1334_2 (Jap_All); LR P-value: 5.24E-16; mr1347_2 (All); LR P-value: 5.71E-12; mr1352_2 (All); LR P-value: 3.01E-16; mr1364_2 (All); LR P-value: 1.06E-12; mr1364_2 (Ind_All); LR P-value: 7.13E-06; mr1388_2 (All); LR P-value: 6.59E-09; mr1425_2 (Jap_All); LR P-value: 8.53E-06; mr1442_2 (Ind_All); LR P-value: 3.68E-06; mr1471_2 (Jap_All); LR P-value: 1.12E-10; mr1526_2 (Jap_All); LR P-value: 4.95E-08; mr1550_2 (Ind_All); LR P-value: 5.03E-06; mr1653_2 (Ind_All); LR P-value: 1.30E-06; mr1671_2 (Jap_All); LR P-value: 8.19E-07; mr1699_2 (Jap_All); LR P-value: 6.66E-17; mr1702_2 (All); LR P-value: 9.87E-06; mr1771_2 (Ind_All); LR P-value: 4.43E-07; mr1784_2 (Ind_All); LR P-value: 4.59E-06; mr1798_2 (Jap_All); LR P-value: 1.00E-06; mr1817_2 (Jap_All); LR P-value: 3.11E-08; mr1991_2 (Jap_All); LR P-value: 5.79E-07; mr1993_2 (All); LR P-value: 1.97E-11 |
LOC_Os01g55630.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 43.280; most accessible tissue: Callus, score: 84.057 |
| vg0132054308 (J) | chr01 | 32054308 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os01g55630.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g55620.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g55640.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g55650.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 42.720; most accessible tissue: Callus, score: 84.057 |
| vg0132054315 (J) | chr01 | 32054315 | G | T | 76.00% | 0.00% | T -> G |
Grain_width (All); LR P-value: 3.61E-57;
mr1010 (All); LR P-value: 2.87E-14; mr1089 (All); LR P-value: 1.06E-43; mr1093 (All); LR P-value: 1.59E-41; mr1163 (All); LR P-value: 4.85E-23; mr1277 (All); LR P-value: 1.21E-10; mr1277 (Jap_All); LR P-value: 9.85E-06; mr1334 (All); LR P-value: 1.39E-86; mr1449 (Jap_All); LR P-value: 1.40E-08; mr1540 (Jap_All); LR P-value: 3.61E-15; mr1551 (Jap_All); LR P-value: 2.34E-07; mr1671 (Jap_All); LR P-value: 1.16E-06; mr1679 (All); LR P-value: 1.31E-20; mr1691 (All); LR P-value: 4.02E-08; mr1693 (All); LR P-value: 2.42E-09; mr1732 (Jap_All); LR P-value: 5.20E-16; mr1740 (All); LR P-value: 1.16E-15; mr1771 (All); LR P-value: 1.09E-47; mr1784 (All); LR P-value: 4.53E-37; mr1785 (All); LR P-value: 2.71E-07; mr1789 (All); LR P-value: 2.50E-29; mr1844 (All); LR P-value: 1.23E-13; mr1896 (Jap_All); LR P-value: 2.00E-06; mr1920 (All); LR P-value: 1.99E-21; mr1019_2 (All); LR P-value: 1.83E-71; mr1089_2 (All); LR P-value: 4.64E-53; mr1093_2 (All); LR P-value: 2.08E-49; mr1097_2 (Jap_All); LR P-value: 1.35E-06; mr1121_2 (Jap_All); LR P-value: 3.14E-06; mr1251_2 (All); LR P-value: 1.86E-37; mr1277_2 (All); LR P-value: 1.17E-14; mr1334_2 (All); LR P-value: 2.76E-100; mr1423_2 (All); LR P-value: 1.95E-29; mr1435_2 (All); LR P-value: 1.51E-37; mr1520_2 (All); LR P-value: 1.18E-11; mr1526_2 (Jap_All); LR P-value: 6.42E-08; mr1539_2 (Jap_All); LR P-value: 2.55E-14; mr1540_2 (Jap_All); LR P-value: 6.04E-15; mr1671_2 (Jap_All); LR P-value: 7.64E-07; mr1679_2 (All); LR P-value: 6.53E-21; mr1732_2 (Jap_All); LR P-value: 1.34E-13; mr1742_2 (Jap_All); LR P-value: 2.55E-09; mr1771_2 (All); LR P-value: 7.71E-41; mr1781_2 (Jap_All); LR P-value: 5.47E-06; mr1784_2 (All); LR P-value: 4.91E-44; mr1800_2 (All); LR P-value: 1.72E-13; mr1862_2 (All); LR P-value: 3.02E-39 |
LOC_Os01g55630.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 42.879; most accessible tissue: Callus, score: 84.057 |
| vg0132054317 (J) | chr01 | 32054317 | G | A | 76.00% | 0.00% | A -> G |
Grain_width (All); LR P-value: 3.61E-57;
mr1010 (All); LR P-value: 2.87E-14; mr1089 (All); LR P-value: 1.06E-43; mr1093 (All); LR P-value: 1.59E-41; mr1163 (All); LR P-value: 4.85E-23; mr1277 (All); LR P-value: 1.21E-10; mr1277 (Jap_All); LR P-value: 9.85E-06; mr1334 (All); LR P-value: 1.39E-86; mr1449 (Jap_All); LR P-value: 1.40E-08; mr1540 (Jap_All); LR P-value: 3.61E-15; mr1551 (Jap_All); LR P-value: 2.34E-07; mr1671 (Jap_All); LR P-value: 1.16E-06; mr1679 (All); LR P-value: 1.31E-20; mr1691 (All); LR P-value: 4.02E-08; mr1693 (All); LR P-value: 2.42E-09; mr1732 (Jap_All); LR P-value: 5.20E-16; mr1740 (All); LR P-value: 1.16E-15; mr1771 (All); LR P-value: 1.09E-47; mr1784 (All); LR P-value: 4.53E-37; mr1785 (All); LR P-value: 2.71E-07; mr1789 (All); LR P-value: 2.50E-29; mr1844 (All); LR P-value: 1.23E-13; mr1896 (Jap_All); LR P-value: 2.00E-06; mr1920 (All); LR P-value: 1.99E-21; mr1019_2 (All); LR P-value: 1.83E-71; mr1089_2 (All); LR P-value: 4.64E-53; mr1093_2 (All); LR P-value: 2.08E-49; mr1097_2 (Jap_All); LR P-value: 1.35E-06; mr1121_2 (Jap_All); LR P-value: 3.14E-06; mr1251_2 (All); LR P-value: 1.86E-37; mr1277_2 (All); LR P-value: 1.17E-14; mr1334_2 (All); LR P-value: 2.76E-100; mr1423_2 (All); LR P-value: 1.95E-29; mr1435_2 (All); LR P-value: 1.51E-37; mr1520_2 (All); LR P-value: 1.18E-11; mr1526_2 (Jap_All); LR P-value: 6.42E-08; mr1539_2 (Jap_All); LR P-value: 2.55E-14; mr1540_2 (Jap_All); LR P-value: 6.04E-15; mr1671_2 (Jap_All); LR P-value: 7.64E-07; mr1679_2 (All); LR P-value: 6.53E-21; mr1732_2 (Jap_All); LR P-value: 1.34E-13; mr1742_2 (Jap_All); LR P-value: 2.55E-09; mr1771_2 (All); LR P-value: 7.71E-41; mr1781_2 (Jap_All); LR P-value: 5.47E-06; mr1784_2 (All); LR P-value: 4.91E-44; mr1800_2 (All); LR P-value: 1.72E-13; mr1862_2 (All); LR P-value: 3.02E-39 |
LOC_Os01g55630.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 42.879; most accessible tissue: Callus, score: 84.057 |
| vg0132054347 (J) | chr01 | 32054347 | A | T | 61.60% | 0.00% | A -> T |
Grain_length (All); LR P-value: 7.67E-15;
Plant_height (Ind_All); LR P-value: 9.06E-16; mr1319 (Ind_All); LR P-value: 4.89E-06; mr1334 (Jap_All); LR P-value: 8.71E-14; mr1352 (Ind_All); LR P-value: 4.33E-06; mr1449 (Jap_All); LR P-value: 1.07E-08; mr1540 (Jap_All); LR P-value: 3.20E-15; mr1633 (Ind_All); LR P-value: 3.12E-06; mr1671 (Jap_All); LR P-value: 1.31E-06; mr1732 (Jap_All); LR P-value: 4.60E-16; mr1742 (All); LR P-value: 6.00E-06; mr1896 (Jap_All); LR P-value: 6.04E-06; mr1045_2 (Ind_All); LR P-value: 8.61E-07; mr1060_2 (Ind_All); LR P-value: 6.96E-06; mr1097_2 (Jap_All); LR P-value: 1.06E-06; mr1115_2 (Ind_All); LR P-value: 1.30E-06; mr1121_2 (Jap_All); LR P-value: 2.49E-06; mr1174_2 (All); LR P-value: 1.92E-11; mr1232_2 (Ind_All); LR P-value: 4.91E-06; mr1268_2 (All); LR P-value: 2.00E-07; mr1268_2 (Ind_All); LR P-value: 1.98E-06; mr1274_2 (Ind_All); LR P-value: 1.17E-06; mr1277_2 (Ind_All); LR P-value: 7.24E-07; mr1319_2 (Ind_All); LR P-value: 9.49E-07; mr1327_2 (All); LR P-value: 1.44E-14; mr1327_2 (Ind_All); LR P-value: 1.95E-12; mr1330_2 (Ind_All); LR P-value: 1.80E-07; mr1334_2 (Jap_All); LR P-value: 7.09E-17; mr1347_2 (All); LR P-value: 5.96E-12; mr1352_2 (All); LR P-value: 6.09E-17; mr1364_2 (All); LR P-value: 1.75E-13; mr1364_2 (Ind_All); LR P-value: 3.67E-06; mr1388_2 (All); LR P-value: 4.02E-09; mr1425_2 (Jap_All); LR P-value: 8.20E-06; mr1442_2 (Ind_All); LR P-value: 2.69E-06; mr1471_2 (Jap_All); LR P-value: 9.38E-11; mr1526_2 (Jap_All); LR P-value: 3.40E-08; mr1539_2 (Jap_All); LR P-value: 4.29E-15; mr1540_2 (Jap_All); LR P-value: 4.15E-15; mr1550_2 (Ind_All); LR P-value: 6.21E-06; mr1653_2 (Ind_All); LR P-value: 1.07E-06; mr1671_2 (Jap_All); LR P-value: 7.24E-07; mr1699_2 (Jap_All); LR P-value: 1.62E-17; mr1702_2 (All); LR P-value: 9.63E-06; mr1732_2 (Jap_All); LR P-value: 1.05E-13; mr1742_2 (Jap_All); LR P-value: 2.95E-09; mr1771_2 (Ind_All); LR P-value: 7.87E-07; mr1771_2 (Jap_All); LR P-value: 9.92E-10; mr1781_2 (Jap_All); LR P-value: 4.18E-06; mr1784_2 (Ind_All); LR P-value: 5.17E-06; mr1784_2 (Jap_All); LR P-value: 1.43E-10; mr1798_2 (Jap_All); LR P-value: 1.51E-06; mr1807_2 (All); LR P-value: 1.18E-13; mr1817_2 (Jap_All); LR P-value: 9.35E-08; mr1862_2 (Jap_All); LR P-value: 7.85E-09; mr1991_2 (Jap_All); LR P-value: 2.29E-07; mr1993_2 (All); LR P-value: 9.38E-12 |
LOC_Os01g55630.1 Alt: T| stop_lost&splice_region_variant HIGH(snpEff)/stop_lost(CooVar)
The average chromatin accessibility score: 40.739; most accessible tissue: Zhenshan97 young leaf, score: 60.208 |