15 variations found. LOC_Os02g35210 (resistance protein; putative; expressed), ranging from 21,166,677 bp to 21,169,952 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0221166710 (J) | chr02 | 21166710 | T | C | 99.60% | 0.00% | T -> C | NA |
LOC_Os02g35210.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os02g35200.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g35220.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 74.442; most accessible tissue: Zhenshan97 young leaf, score: 88.259 |
| vg0221166729 (J) | chr02 | 21166729 | A | G | 59.20% | 0.06% | G -> A |
mr1109 (All); LR P-value: 5.22E-55;
mr1129 (All); LR P-value: 5.01E-33; mr1144 (All); LR P-value: 6.40E-42; mr1164 (All); LR P-value: 1.30E-14; mr1243 (All); LR P-value: 6.16E-31; mr1251 (All); LR P-value: 7.17E-27; mr1255 (All); LR P-value: 3.53E-19; mr1257 (All); LR P-value: 1.32E-32; mr1435 (All); LR P-value: 5.04E-37; mr1551 (All); LR P-value: 3.05E-25; mr1720 (All); LR P-value: 5.42E-11; mr1793 (All); LR P-value: 8.05E-29; mr1870 (All); LR P-value: 7.92E-15; mr1037_2 (All); LR P-value: 1.72E-31; mr1109_2 (All); LR P-value: 3.70E-65; mr1129_2 (All); LR P-value: 5.09E-37; mr1208_2 (All); LR P-value: 1.77E-36; mr1251_2 (All); LR P-value: 1.38E-36; mr1257_2 (All); LR P-value: 3.85E-36; mr1350_2 (All); LR P-value: 9.62E-24; mr1435_2 (All); LR P-value: 1.65E-36; mr1720_2 (All); LR P-value: 1.53E-15; mr1793_2 (All); LR P-value: 1.79E-45 |
LOC_Os02g35210.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g35210.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 73.614; most accessible tissue: Zhenshan97 young leaf, score: 89.112 |
| vg0221167230 (J) | chr02 | 21167230 | G | A | 98.00% | 0.00% | G -> A | NA |
LOC_Os02g35210.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 71.530; most accessible tissue: Minghui63 flag leaf, score: 84.420 |
| vg0221167251 (J) | chr02 | 21167251 | C | T | 66.20% | 0.17% | T -> C |
mr1014 (All); LR P-value: 1.18E-70;
mr1027 (All); LR P-value: 2.81E-66; mr1100 (All); LR P-value: 6.21E-77; mr1105 (All); LR P-value: 3.66E-37; mr1134 (All); LR P-value: 1.74E-86; mr1136 (All); LR P-value: 9.17E-53; mr1140 (All); LR P-value: 4.44E-91; mr1162 (All); LR P-value: 3.41E-07; mr1194 (All); LR P-value: 2.01E-49; mr1203 (All); LR P-value: 1.71E-95; mr1238 (All); LR P-value: 2.78E-26; mr1243 (All); LR P-value: 7.54E-33; mr1309 (All); LR P-value: 1.86E-28; mr1383 (All); LR P-value: 5.26E-24; mr1395 (All); LR P-value: 7.04E-90; mr1480 (All); LR P-value: 1.02E-45; mr1484 (All); LR P-value: 1.33E-15; mr1548 (All); LR P-value: 1.62E-22; mr1566 (All); LR P-value: 2.83E-17; mr1591 (All); LR P-value: 2.12E-43; mr1594 (All); LR P-value: 1.68E-57; mr1613 (All); LR P-value: 1.70E-77; mr1618 (All); LR P-value: 5.46E-95; mr1629 (All); LR P-value: 4.74E-78; mr1672 (All); LR P-value: 5.32E-85; mr1692 (All); LR P-value: 8.99E-57; mr1711 (All); LR P-value: 1.19E-60; mr1715 (All); LR P-value: 2.59E-19; mr1758 (All); LR P-value: 6.39E-86; mr1767 (All); LR P-value: 9.43E-18; mr1828 (All); LR P-value: 5.97E-36; mr1888 (All); LR P-value: 1.62E-24; mr1932 (All); LR P-value: 1.51E-33; mr1944 (All); LR P-value: 1.51E-33; mr1968 (All); LR P-value: 1.18E-17; mr1071_2 (All); LR P-value: 3.35E-105; mr1080_2 (All); LR P-value: 2.54E-101; mr1100_2 (All); LR P-value: 1.09E-99; mr1105_2 (All); LR P-value: 1.74E-34; mr1134_2 (All); LR P-value: 1.47E-105; mr1136_2 (All); LR P-value: 7.79E-59; mr1175_2 (All); LR P-value: 5.32E-21; mr1194_2 (All); LR P-value: 6.54E-55; mr1203_2 (All); LR P-value: 5.13E-113; mr1232_2 (All); LR P-value: 1.64E-09; mr1238_2 (All); LR P-value: 1.71E-28; mr1243_2 (All); LR P-value: 1.10E-39; mr1258_2 (All); LR P-value: 5.85E-12; mr1379_2 (All); LR P-value: 5.83E-09; mr1383_2 (All); LR P-value: 3.07E-19; mr1402_2 (All); LR P-value: 1.14E-63; mr1416_2 (All); LR P-value: 2.10E-17; mr1448_2 (All); LR P-value: 1.69E-35; mr1480_2 (All); LR P-value: 3.29E-53; mr1484_2 (All); LR P-value: 2.69E-25; mr1529_2 (All); LR P-value: 1.96E-14; mr1557_2 (All); LR P-value: 2.51E-17; mr1599_2 (All); LR P-value: 6.89E-59; mr1613_2 (All); LR P-value: 2.50E-123; mr1619_2 (All); LR P-value: 1.14E-98; mr1629_2 (All); LR P-value: 5.79E-103; mr1636_2 (All); LR P-value: 5.06E-12; mr1653_2 (All); LR P-value: 1.76E-24; mr1695_2 (All); LR P-value: 1.41E-56; mr1711_2 (All); LR P-value: 6.96E-82; mr1715_2 (All); LR P-value: 7.56E-17; mr1767_2 (All); LR P-value: 3.50E-17; mr1780_2 (All); LR P-value: 2.17E-32; mr1828_2 (All); LR P-value: 3.10E-70; mr1838_2 (All); LR P-value: 1.58E-13; mr1841_2 (All); LR P-value: 4.95E-32; mr1944_2 (All); LR P-value: 5.84E-42; mr1945_2 (All); LR P-value: 3.91E-18; mr1968_2 (All); LR P-value: 5.62E-23 |
LOC_Os02g35210.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g35210.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 72.531; most accessible tissue: Minghui63 flag leaf, score: 86.468 |
| vg0221167589 (J) | chr02 | 21167589 | A | G | 97.90% | 0.00% | A -> G | NA |
LOC_Os02g35200.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35220.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35210.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 52.637; most accessible tissue: Minghui63 flag leaf, score: 67.099 |
| vg0221167629 (J) | chr02 | 21167629 | A | G | 93.10% | 0.00% | A -> G |
mr1612 (All); LR P-value: 5.30E-14;
mr1098_2 (All); LR P-value: 4.96E-29; mr1099_2 (All); LR P-value: 9.76E-26; mr1113_2 (All); LR P-value: 3.02E-18; mr1114_2 (All); LR P-value: 5.34E-17; mr1117_2 (All); LR P-value: 2.27E-20; mr1119_2 (All); LR P-value: 1.29E-19; mr1120_2 (All); LR P-value: 3.13E-25; mr1123_2 (All); LR P-value: 6.49E-25; mr1166_2 (All); LR P-value: 7.25E-10; mr1240_2 (All); LR P-value: 1.64E-18; mr1247_2 (All); LR P-value: 1.20E-25; mr1496_2 (All); LR P-value: 1.06E-13; mr1612_2 (All); LR P-value: 1.90E-09; mr1936_2 (All); LR P-value: 7.75E-17; mr1961_2 (All); LR P-value: 2.15E-15 |
LOC_Os02g35200.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35220.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35210.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.289; most accessible tissue: Minghui63 flag leaf, score: 71.116 |
| vg0221167643 (J) | chr02 | 21167643 | G | A | 59.10% | 0.06% | A -> G |
mr1109 (All); LR P-value: 1.47E-54;
mr1129 (All); LR P-value: 2.03E-32; mr1144 (All); LR P-value: 4.79E-43; mr1164 (All); LR P-value: 4.25E-15; mr1243 (All); LR P-value: 5.62E-31; mr1251 (All); LR P-value: 2.34E-26; mr1255 (All); LR P-value: 3.97E-19; mr1257 (All); LR P-value: 3.90E-32; mr1435 (All); LR P-value: 1.87E-36; mr1551 (All); LR P-value: 1.31E-25; mr1720 (All); LR P-value: 5.12E-11; mr1756 (All); LR P-value: 1.46E-06; mr1793 (All); LR P-value: 4.53E-28; mr1037_2 (All); LR P-value: 5.08E-32; mr1094_2 (All); LR P-value: 1.61E-44; mr1109_2 (All); LR P-value: 5.39E-64; mr1129_2 (All); LR P-value: 1.99E-36; mr1257_2 (All); LR P-value: 1.71E-35; mr1720_2 (All); LR P-value: 1.29E-15 |
LOC_Os02g35200.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35220.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35210.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 54.977; most accessible tissue: Minghui63 flag leaf, score: 73.752 |
| vg0221167646 (J) | chr02 | 21167646 | C | T | 66.10% | 0.08% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g35200.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35220.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35210.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.042; most accessible tissue: Minghui63 flag leaf, score: 68.675 |
| vg0221167853 (J) | chr02 | 21167853 | TA | T | 34.50% | 44.48% | TA -> T | NA |
LOC_Os02g35200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35220.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35210.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 53.805; most accessible tissue: Minghui63 flag leaf, score: 73.752 |
| vg0221167854 (J) | chr02 | 21167854 | A | AT | 68.40% | 0.00% | AT -> A | NA |
LOC_Os02g35200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35220.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35210.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 52.822; most accessible tissue: Minghui63 flag leaf, score: 73.334 |
| vg0221168365 (J) | chr02 | 21168365 | A | G | 93.10% | 0.00% | A -> G |
mr1612 (All); LR P-value: 1.17E-13;
mr1706 (All); LR P-value: 5.68E-07; mr1099_2 (All); LR P-value: 6.41E-24; mr1113_2 (All); LR P-value: 1.28E-17; mr1114_2 (All); LR P-value: 1.78E-16; mr1117_2 (All); LR P-value: 5.72E-20; mr1119_2 (All); LR P-value: 4.36E-19; mr1120_2 (All); LR P-value: 3.25E-24; mr1123_2 (All); LR P-value: 2.38E-24; mr1166_2 (All); LR P-value: 1.26E-09; mr1240_2 (All); LR P-value: 7.28E-18; mr1247_2 (All); LR P-value: 2.21E-24; mr1496_2 (All); LR P-value: 4.38E-13; mr1582_2 (All); LR P-value: 2.23E-07; mr1612_2 (All); LR P-value: 1.36E-09; mr1936_2 (All); LR P-value: 6.06E-16; mr1961_2 (All); LR P-value: 9.17E-15 |
LOC_Os02g35210.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 62.983; most accessible tissue: Minghui63 flag leaf, score: 81.312 |
| vg0221169385 (J) | chr02 | 21169385 | C | T | 66.30% | 0.00% | T -> C | NA |
LOC_Os02g35210.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 64.926; most accessible tissue: Minghui63 flag leaf, score: 80.786 |
| vg0221169395 (J) | chr02 | 21169395 | A | T | 99.80% | 0.00% | A -> T | NA |
LOC_Os02g35210.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os02g35200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g35220.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 63.949; most accessible tissue: Minghui63 flag leaf, score: 78.782 |
| vg0221169593 (J) | chr02 | 21169593 | T | A | 99.90% | 0.00% | T -> A | NA |
LOC_Os02g35210.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os02g35200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g35220.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 59.983; most accessible tissue: Minghui63 flag leaf, score: 80.786 |
| STR0221167855 (J) | chr02 | 21167855 | TT | TTT | 68.30% | 0.00% | TTT -> TT | NA |
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