23 variations found. LOC_Os02g56050 (rhodanese-like domain containing protein; putative; expressed), ranging from 34,309,674 bp to 34,311,183 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0234309888 (J) | chr02 | 34309888 | C | A | 82.50% | 0.28% | C -> A | NA |
LOC_Os02g56050.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g56050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.397; most accessible tissue: Zhenshan97 young leaf, score: 92.356 |
| vg0234309940 (J) | chr02 | 34309940 | T | A | 52.70% | 0.00% | T -> A |
mr1294_2 (All); LR P-value: 4.57E-06;
mr1418_2 (All); LR P-value: 3.67E-08; mr1420_2 (All); LR P-value: 7.62E-06; mr1488_2 (All); LR P-value: 4.52E-07; mr1497_2 (All); LR P-value: 6.68E-06; mr1506_2 (All); LR P-value: 7.46E-10; mr1604_2 (All); LR P-value: 2.28E-07; mr1659_2 (All); LR P-value: 1.34E-10; mr1992_2 (All); LR P-value: 2.30E-06 |
LOC_Os02g56050.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 83.520; most accessible tissue: Zhenshan97 young leaf, score: 91.967 |
| vg0234309998 (J) | chr02 | 34309998 | C | T | 52.70% | 0.17% | C -> T |
mr1041_2 (All); LR P-value: 8.87E-06;
mr1232_2 (All); LR P-value: 2.66E-09; mr1294_2 (All); LR P-value: 4.41E-06; mr1418_2 (All); LR P-value: 3.24E-08; mr1420_2 (All); LR P-value: 6.52E-06; mr1488_2 (All); LR P-value: 4.66E-07; mr1497_2 (All); LR P-value: 7.44E-06; mr1506_2 (All); LR P-value: 6.24E-10; mr1604_2 (All); LR P-value: 1.44E-07; mr1659_2 (All); LR P-value: 5.32E-11; mr1992_2 (All); LR P-value: 2.31E-06 |
LOC_Os02g56050.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g56050.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 81.838; most accessible tissue: Minghui63 flag leaf, score: 89.812 |
| vg0234310055 (J) | chr02 | 34310055 | G | A | 82.00% | 0.00% | G -> A | NA |
LOC_Os02g56050.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 79.927; most accessible tissue: Minghui63 flag leaf, score: 88.798 |
| vg0234310209 (J) | chr02 | 34310209 | C | T | 52.70% | 0.34% | C -> T |
mr1041_2 (All); LR P-value: 8.56E-06;
mr1294_2 (All); LR P-value: 5.29E-06; mr1418_2 (All); LR P-value: 2.93E-08; mr1420_2 (All); LR P-value: 5.39E-06; mr1488_2 (All); LR P-value: 3.72E-07; mr1497_2 (All); LR P-value: 9.55E-06; mr1506_2 (All); LR P-value: 6.82E-10; mr1604_2 (All); LR P-value: 1.87E-07; mr1659_2 (All); LR P-value: 6.59E-11; mr1992_2 (All); LR P-value: 1.96E-06 |
LOC_Os02g56040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 66.953; most accessible tissue: Callus, score: 77.368 |
| vg0234310220 (J) | chr02 | 34310220 | G | A | 62.00% | 0.00% | G -> A |
LOC_Os02g56040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.412; most accessible tissue: Callus, score: 77.368 |
|
| vg0234310447 (J) | chr02 | 34310447 | ACTC | A | 98.10% | 0.00% | ACTC -> A | NA |
LOC_Os02g56050.1 Alt: A| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 55.080; most accessible tissue: Callus, score: 80.669 |
| vg0234310559 (J) | chr02 | 34310559 | A | T | 97.50% | 0.00% | A -> T | NA |
LOC_Os02g56040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.458; most accessible tissue: Callus, score: 80.669 |
| vg0234310701 (J) | chr02 | 34310701 | C | CA | 99.70% | 0.00% | C -> CA | NA |
LOC_Os02g56040.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g56060.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g56050.1 Alt: CA| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 45.285; most accessible tissue: Callus, score: 83.150 |
| vg0234310744 (J) | chr02 | 34310744 | G | A | 51.70% | 0.02% | G -> A |
mr1041_2 (All); LR P-value: 7.61E-06;
mr1294_2 (All); LR P-value: 3.50E-06; mr1418_2 (All); LR P-value: 3.84E-08; mr1420_2 (All); LR P-value: 6.39E-06; mr1488_2 (All); LR P-value: 4.23E-07; mr1497_2 (All); LR P-value: 2.22E-06; mr1506_2 (All); LR P-value: 1.16E-09; mr1604_2 (All); LR P-value: 3.00E-07; mr1659_2 (All); LR P-value: 5.14E-10; mr1779_2 (All); LR P-value: 7.06E-06; mr1992_2 (All); LR P-value: 1.73E-06 |
LOC_Os02g56040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 43.899; most accessible tissue: Callus, score: 83.150 |
| vg0234310759 (J) | chr02 | 34310759 | G | A | 51.80% | 0.19% | G -> A |
mr1041_2 (All); LR P-value: 8.42E-06;
mr1294_2 (All); LR P-value: 3.95E-06; mr1418_2 (All); LR P-value: 4.43E-08; mr1420_2 (All); LR P-value: 6.99E-06; mr1488_2 (All); LR P-value: 4.59E-07; mr1497_2 (All); LR P-value: 2.47E-06; mr1506_2 (All); LR P-value: 1.29E-09; mr1604_2 (All); LR P-value: 3.11E-07; mr1659_2 (All); LR P-value: 4.45E-10; mr1779_2 (All); LR P-value: 7.34E-06; mr1992_2 (All); LR P-value: 1.70E-06 |
LOC_Os02g56040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 45.297; most accessible tissue: Callus, score: 83.150 |
| vg0234310843 (J) | chr02 | 34310843 | T | C | 68.30% | 0.00% | C -> T |
mr1018 (All); LR P-value: 2.41E-73;
mr1019 (All); LR P-value: 1.30E-56; mr1071 (All); LR P-value: 3.42E-91; mr1080 (All); LR P-value: 9.16E-82; mr1100 (All); LR P-value: 1.61E-77; mr1140 (All); LR P-value: 7.45E-92; mr1203 (All); LR P-value: 6.74E-98; mr1529 (All); LR P-value: 3.74E-18; mr1613 (All); LR P-value: 1.82E-76; mr1618 (All); LR P-value: 2.80E-92; mr1698 (All); LR P-value: 8.21E-23; mr1737 (All); LR P-value: 2.40E-29; mr1905 (All); LR P-value: 3.59E-10; mr1019_2 (All); LR P-value: 2.00E-69; mr1024_2 (All); LR P-value: 1.21E-24; mr1042_2 (All); LR P-value: 3.20E-21; mr1071_2 (All); LR P-value: 2.02E-108; mr1080_2 (All); LR P-value: 1.03E-103; mr1100_2 (All); LR P-value: 9.80E-99; mr1105_2 (All); LR P-value: 5.22E-30; mr1146_2 (All); LR P-value: 5.48E-17; mr1150_2 (All); LR P-value: 2.33E-31; mr1167_2 (All); LR P-value: 2.00E-20; mr1194_2 (All); LR P-value: 1.12E-51; mr1203_2 (All); LR P-value: 3.90E-116; mr1239_2 (All); LR P-value: 2.54E-18; mr1258_2 (All); LR P-value: 6.05E-12; mr1275_2 (All); LR P-value: 1.54E-06; mr1298_2 (All); LR P-value: 7.58E-21; mr1386_2 (All); LR P-value: 1.14E-23; mr1613_2 (All); LR P-value: 1.68E-124; mr1641_2 (All); LR P-value: 5.73E-12; mr1698_2 (All); LR P-value: 3.93E-25; mr1711_2 (All); LR P-value: 9.43E-82; mr1714_2 (All); LR P-value: 1.99E-11; mr1726_2 (All); LR P-value: 2.09E-16; mr1731_2 (All); LR P-value: 6.15E-20; mr1761_2 (All); LR P-value: 6.74E-10; mr1767_2 (All); LR P-value: 3.60E-15; mr1866_2 (All); LR P-value: 5.18E-15; mr1950_2 (All); LR P-value: 7.52E-15 |
LOC_Os02g56040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 38.713; most accessible tissue: Callus, score: 59.390 |
| vg0234310846 (J) | chr02 | 34310846 | T | C | 51.80% | 0.00% | T -> C |
mr1041_2 (All); LR P-value: 3.63E-06;
mr1293_2 (All); LR P-value: 6.09E-06; mr1294_2 (All); LR P-value: 2.52E-06; mr1418_2 (All); LR P-value: 2.13E-08; mr1420_2 (All); LR P-value: 4.60E-06; mr1488_2 (All); LR P-value: 2.71E-07; mr1497_2 (All); LR P-value: 1.73E-06; mr1506_2 (All); LR P-value: 8.16E-10; mr1604_2 (All); LR P-value: 1.53E-07; mr1659_2 (All); LR P-value: 5.58E-10; mr1779_2 (All); LR P-value: 5.22E-06; mr1992_2 (All); LR P-value: 1.01E-06 |
LOC_Os02g56040.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 39.339; most accessible tissue: Callus, score: 59.390 |
| vg0234310851 (J) | chr02 | 34310851 | G | A | 99.00% | 0.00% | G -> A | NA |
LOC_Os02g56040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 39.396; most accessible tissue: Callus, score: 59.390 |
| vg0234310872 (J) | chr02 | 34310872 | T | TA | 68.00% | 0.00% | TA -> T | NA |
LOC_Os02g56040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.761; most accessible tissue: Callus, score: 59.390 |
| vg0234310881 (J) | chr02 | 34310881 | G | A | 82.80% | 0.00% | G -> A | NA |
LOC_Os02g56040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 36.770; most accessible tissue: Callus, score: 59.390 |
| vg0234310882 (J) | chr02 | 34310882 | G | A | 68.30% | 0.00% | A -> G |
Grain_width (All); LR P-value: 2.35E-53;
mr1018 (All); LR P-value: 2.53E-74; mr1019 (All); LR P-value: 4.52E-57; mr1071 (All); LR P-value: 1.57E-91; mr1080 (All); LR P-value: 6.15E-81; mr1100 (All); LR P-value: 2.24E-78; mr1140 (All); LR P-value: 3.04E-92; mr1203 (All); LR P-value: 6.99E-98; mr1529 (All); LR P-value: 1.75E-18; mr1613 (All); LR P-value: 4.20E-77; mr1618 (All); LR P-value: 4.44E-92; mr1629 (All); LR P-value: 6.61E-74; mr1698 (All); LR P-value: 4.81E-22; mr1905 (All); LR P-value: 3.17E-10; mr1019_2 (All); LR P-value: 1.39E-69; mr1024_2 (All); LR P-value: 5.47E-25; mr1042_2 (All); LR P-value: 2.39E-21; mr1071_2 (All); LR P-value: 1.25E-107; mr1080_2 (All); LR P-value: 4.40E-103; mr1100_2 (All); LR P-value: 7.13E-100; mr1102_2 (All); LR P-value: 1.23E-30; mr1133_2 (All); LR P-value: 1.78E-14; mr1146_2 (All); LR P-value: 4.69E-17; mr1150_2 (All); LR P-value: 3.31E-31; mr1167_2 (All); LR P-value: 3.61E-19; mr1168_2 (All); LR P-value: 2.45E-18; mr1194_2 (All); LR P-value: 5.15E-52; mr1203_2 (All); LR P-value: 9.39E-116; mr1223_2 (All); LR P-value: 3.73E-35; mr1227_2 (All); LR P-value: 2.59E-06; mr1239_2 (All); LR P-value: 1.77E-18; mr1258_2 (All); LR P-value: 3.74E-12; mr1275_2 (All); LR P-value: 9.87E-07; mr1298_2 (All); LR P-value: 3.81E-21; mr1386_2 (All); LR P-value: 8.00E-24; mr1479_2 (All); LR P-value: 2.40E-06; mr1613_2 (All); LR P-value: 2.95E-125; mr1636_2 (All); LR P-value: 1.43E-11; mr1641_2 (All); LR P-value: 5.19E-12; mr1681_2 (All); LR P-value: 1.40E-07; mr1698_2 (All); LR P-value: 9.53E-24; mr1711_2 (All); LR P-value: 7.36E-83; mr1714_2 (All); LR P-value: 8.99E-12; mr1726_2 (All); LR P-value: 6.23E-16; mr1730_2 (All); LR P-value: 4.69E-17; mr1731_2 (All); LR P-value: 4.09E-20; mr1767_2 (All); LR P-value: 2.47E-15; mr1866_2 (All); LR P-value: 8.25E-16; mr1909_2 (All); LR P-value: 1.25E-07; mr1921_2 (All); LR P-value: 1.97E-07; mr1950_2 (All); LR P-value: 6.75E-14 |
LOC_Os02g56040.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 37.435; most accessible tissue: Callus, score: 59.390 |
| vg0234310894 (J) | chr02 | 34310894 | G | A | 97.50% | 0.00% | G -> A | NA |
LOC_Os02g56040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 36.789; most accessible tissue: Callus, score: 59.390 |
| vg0234310971 (J) | chr02 | 34310971 | A | T | 99.80% | 0.00% | A -> T | NA |
LOC_Os02g56040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g56060.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g56050.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 36.478; most accessible tissue: Callus, score: 76.724 |
| vg0234311021 (J) | chr02 | 34311021 | T | G | 91.50% | 0.00% | T -> G |
mr1032 (Ind_All); LR P-value: 4.86E-07;
mr1165 (Ind_All); LR P-value: 9.96E-07; mr1415 (Ind_All); LR P-value: 7.94E-06; mr1478 (Ind_All); LR P-value: 1.28E-06; mr1567 (Ind_All); LR P-value: 7.94E-06; mr1664 (All); LMM P-value: 3.57E-06; LR P-value: 3.57E-06; mr1664 (Ind_All); LMM P-value: 4.09E-06; LR P-value: 4.09E-06; mr1829 (Ind_All); LR P-value: 2.27E-09; mr1165_2 (Ind_All); LR P-value: 9.53E-07; mr1478_2 (Ind_All); LR P-value: 1.65E-09; mr1971_2 (Ind_All); LR P-value: 4.26E-07 |
LOC_Os02g56040.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 35.041; most accessible tissue: Callus, score: 76.724 |
| vg0234311101 (J) | chr02 | 34311101 | A | T | 99.00% | 0.00% | A -> T | NA |
LOC_Os02g56040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 34.030; most accessible tissue: Callus, score: 47.253 |
| vg0234311127 (J) | chr02 | 34311127 | A | G | 82.60% | 0.08% | A -> G | NA |
LOC_Os02g56040.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56060.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56050.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 33.793; most accessible tissue: Callus, score: 47.253 |
| STR0234310865 (J) | chr02 | 34310865 | TT | TTT | 65.90% | 0.00% | TTT -> TT | NA |
|