15 variations found. LOC_Os04g50188 (retrotransposon protein; putative; unclassified; expressed), ranging from 29,945,953 bp to 29,946,289 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 |
---|---|---|---|---|---|---|---|---|---|
vg0429945960 (J) | chr04 | 29945960 | A | G | 84.00% | 0.00% | A -> G |
mr1138 (All); LR P-value: 4.40E-14;
mr1138 (Ind_All); LR P-value: 7.90E-09; mr1169 (All); LMM P-value: 5.10E-06; LR P-value: 7.93E-20; mr1169 (Ind_All); LMM P-value: 4.78E-06; LR P-value: 1.89E-12; mr1174 (All); LMM P-value: 2.62E-11; LR P-value: 1.07E-25; mr1174 (Ind_All); LMM P-value: 5.08E-13; LR P-value: 5.59E-24; mr1347 (All); LMM P-value: 7.34E-09; LR P-value: 5.64E-14; mr1347 (Ind_All); LMM P-value: 1.12E-08; LR P-value: 1.13E-14; mr1354 (All); LR P-value: 1.08E-08; mr1354 (Ind_All); LR P-value: 7.73E-09; mr1406 (Ind_All); LR P-value: 7.57E-08; mr1138_2 (All); LMM P-value: 1.80E-06; LR P-value: 1.12E-15; mr1138_2 (Ind_All); LMM P-value: 6.86E-06; LR P-value: 1.93E-09; mr1174_2 (All); LMM P-value: 1.76E-07; LR P-value: 2.34E-24; mr1174_2 (Ind_All); LMM P-value: 3.91E-09; LR P-value: 1.92E-23; mr1347_2 (All); LMM P-value: 4.22E-08; LR P-value: 2.20E-19; mr1347_2 (Ind_All); LMM P-value: 7.49E-07; LR P-value: 3.39E-20; mr1349_2 (Ind_All); LR P-value: 4.74E-06; mr1354_2 (All); LR P-value: 1.21E-11; mr1354_2 (Ind_All); LMM P-value: 2.93E-06; LR P-value: 1.47E-12; mr1406_2 (Ind_All); LR P-value: 1.75E-06; mr1540_2 (Ind_All); LR P-value: 4.23E-06; mr1732_2 (Ind_All); LR P-value: 2.02E-06 |
LOC_Os04g50188.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 50.943; most accessible tissue: Zhenshan97 panicle, score: 61.671 |
vg0429945982 (J) | chr04 | 29945982 | C | T | 95.20% | 0.00% | C -> T |
mr1248 (All); LR P-value: 6.35E-08;
mr1248 (Jap_All); LR P-value: 1.21E-09; mr1518 (Jap_All); LR P-value: 3.83E-06; mr1676 (Jap_All); LR P-value: 2.51E-06; mr1769 (All); LR P-value: 8.03E-12; mr1676_2 (Jap_All); LR P-value: 3.37E-08; mr1769_2 (All); LR P-value: 3.33E-13; mr1769_2 (Jap_All); LR P-value: 8.43E-13 |
LOC_Os04g50188.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 50.035; most accessible tissue: Zhenshan97 panicle, score: 61.671 |
vg0429945986 (J) | chr04 | 29945986 | T | A | 94.10% | 0.00% | T -> A | NA |
LOC_Os04g50188.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 49.994; most accessible tissue: Zhenshan97 panicle, score: 61.671 |
vg0429945987 (J) | chr04 | 29945987 | C | T | 89.30% | 0.00% | C -> T |
mr1136 (All); LMM P-value: 5.33E-07;
mr1248 (Jap_All); LR P-value: 2.04E-09; mr1518 (Jap_All); LR P-value: 3.24E-06; mr1676 (Jap_All); LR P-value: 2.34E-06; mr1769 (All); LR P-value: 1.57E-11; mr1769 (Jap_All); LR P-value: 1.08E-13; mr1951 (All); LR P-value: 1.47E-07; mr1951 (Jap_All); LR P-value: 7.69E-07; mr1082_2 (All); LMM P-value: 5.07E-06; mr1226_2 (All); LMM P-value: 4.39E-06; mr1632_2 (Jap_All); LR P-value: 1.07E-06; mr1676_2 (Jap_All); LR P-value: 4.13E-09; mr1769_2 (All); LR P-value: 1.05E-11; mr1769_2 (Jap_All); LR P-value: 6.24E-15 |
LOC_Os04g50188.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g50188.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 50.544; most accessible tissue: Minghui63 panicle, score: 62.157 |
vg0429945988 (J) | chr04 | 29945988 | G | A | 90.30% | 0.00% | G -> A |
mr1248 (All); LMM P-value: 8.96E-06; LR P-value: 2.11E-10;
mr1248 (Jap_All); LR P-value: 4.07E-10; mr1518 (Jap_All); LR P-value: 3.28E-06; mr1676 (Jap_All); LR P-value: 1.28E-06; mr1769 (Jap_All); LR P-value: 6.22E-14; mr1951 (Jap_All); LR P-value: 1.57E-07; mr1510_2 (Jap_All); LR P-value: 2.88E-06; mr1632_2 (Jap_All); LR P-value: 3.91E-07; mr1676_2 (Jap_All); LR P-value: 1.12E-09; mr1696_2 (All); LR P-value: 6.58E-07; mr1769_2 (Jap_All); LR P-value: 7.03E-14 |
LOC_Os04g50188.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 50.026; most accessible tissue: Minghui63 panicle, score: 62.157 |
vg0429946010 (J) | chr04 | 29946010 | T | G | 94.10% | 0.00% | T -> G | NA |
LOC_Os04g50188.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 49.644; most accessible tissue: Minghui63 panicle, score: 62.157 |
vg0429946012 (J) | chr04 | 29946012 | G | C | 94.10% | 0.00% | G -> C | NA |
LOC_Os04g50188.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 50.423; most accessible tissue: Zhenshan97 panicle, score: 63.607 |
vg0429946042 (J) | chr04 | 29946042 | A | G | 74.90% | 0.25% | A -> G |
mr1169 (Ind_All); LR P-value: 1.37E-11;
mr1174 (All); LMM P-value: 4.07E-07; LR P-value: 4.06E-17; mr1174 (Ind_All); LMM P-value: 3.14E-10; LR P-value: 3.74E-21; mr1347 (All); LMM P-value: 7.25E-06; LR P-value: 7.74E-09; mr1347 (Ind_All); LMM P-value: 7.75E-08; LR P-value: 6.42E-14; mr1354 (Ind_All); LR P-value: 2.93E-07; mr1406 (Ind_All); LMM P-value: 8.05E-06; LR P-value: 5.21E-09; mr1174_2 (All); LMM P-value: 1.36E-06; LR P-value: 8.92E-15; mr1174_2 (Ind_All); LMM P-value: 2.79E-11; LR P-value: 4.18E-25; mr1347_2 (All); LMM P-value: 7.54E-08; LR P-value: 6.68E-11; mr1347_2 (Ind_All); LMM P-value: 2.66E-11; LR P-value: 1.18E-23; mr1354_2 (Ind_All); LR P-value: 8.32E-09; mr1406_2 (Ind_All); LMM P-value: 8.12E-06; LR P-value: 3.37E-09; mr1540_2 (Ind_All); LR P-value: 1.58E-06; mr1732_2 (Ind_All); LR P-value: 2.04E-06 |
LOC_Os04g50188.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g50188.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 51.023; most accessible tissue: Zhenshan97 panicle, score: 63.607 |
vg0429946046 (J) | chr04 | 29946046 | C | T | 94.10% | 0.00% | C -> T |
mr1117 (Jap_All); LR P-value: 4.95E-06;
mr1745 (Jap_All); LR P-value: 2.79E-07; mr1117_2 (Jap_All); LR P-value: 3.21E-07; mr1119_2 (Jap_All); LR P-value: 9.54E-07; mr1240_2 (Jap_All); LR P-value: 2.15E-06; mr1496_2 (Jap_All); LR P-value: 6.27E-06; mr1519_2 (Jap_All); LR P-value: 9.91E-06; mr1745_2 (Jap_All); LR P-value: 5.47E-06 |
LOC_Os04g50188.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 51.288; most accessible tissue: Zhenshan97 panicle, score: 63.607 |
vg0429946080 (J) | chr04 | 29946080 | C | T | 74.90% | 0.53% | C -> T |
mr1138 (Ind_All); LR P-value: 8.37E-06;
mr1169 (Ind_All); LMM P-value: 1.33E-06; LR P-value: 1.82E-13; mr1174 (All); LMM P-value: 1.04E-06; LR P-value: 2.81E-16; mr1174 (Ind_All); LMM P-value: 2.58E-10; LR P-value: 1.67E-20; mr1347 (All); LR P-value: 1.16E-07; mr1347 (Ind_All); LMM P-value: 2.85E-06; LR P-value: 6.38E-12; mr1354 (Ind_All); LR P-value: 1.26E-08; mr1406 (Ind_All); LR P-value: 5.20E-07; mr1531 (Ind_All); LR P-value: 4.68E-06; mr1138_2 (Ind_All); LR P-value: 7.82E-06; mr1174_2 (All); LMM P-value: 7.39E-07; LR P-value: 1.37E-14; mr1174_2 (Ind_All); LMM P-value: 2.22E-11; LR P-value: 1.01E-23; mr1347_2 (All); LMM P-value: 3.60E-07; LR P-value: 2.91E-10; mr1347_2 (Ind_All); LMM P-value: 8.79E-10; LR P-value: 9.08E-21; mr1354_2 (Ind_All); LR P-value: 1.01E-09; mr1406_2 (Ind_All); LR P-value: 1.73E-08; mr1540_2 (Ind_All); LR P-value: 1.85E-07; mr1732_2 (Ind_All); LR P-value: 2.30E-07 |
LOC_Os04g50188.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g50188.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 51.974; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
vg0429946087 (J) | chr04 | 29946087 | C | T | 74.80% | 0.53% | C -> T |
mr1138 (Ind_All); LR P-value: 6.81E-06;
mr1169 (Ind_All); LMM P-value: 3.52E-06; LR P-value: 6.08E-13; mr1174 (All); LMM P-value: 5.78E-08; LR P-value: 6.75E-18; mr1174 (Ind_All); LMM P-value: 7.60E-12; LR P-value: 8.76E-23; mr1347 (All); LR P-value: 6.84E-08; mr1347 (Ind_All); LMM P-value: 2.11E-06; LR P-value: 2.38E-12; mr1354 (Ind_All); LR P-value: 6.65E-09; mr1406 (Ind_All); LR P-value: 2.50E-07; mr1531 (Ind_All); LR P-value: 4.59E-06; mr1138_2 (Ind_All); LR P-value: 3.80E-06; mr1174_2 (All); LMM P-value: 1.68E-06; LR P-value: 3.42E-14; mr1174_2 (Ind_All); LMM P-value: 1.49E-11; LR P-value: 2.61E-24; mr1347_2 (All); LMM P-value: 1.51E-06; LR P-value: 1.23E-09; mr1347_2 (Ind_All); LMM P-value: 9.92E-10; LR P-value: 6.72E-21; mr1354_2 (Ind_All); LR P-value: 2.33E-10; mr1406_2 (Ind_All); LR P-value: 1.51E-08; mr1540_2 (Ind_All); LR P-value: 7.24E-07; mr1732_2 (Ind_All); LR P-value: 8.17E-07 |
LOC_Os04g50188.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g50188.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 51.941; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
vg0429946123 (J) | chr04 | 29946123 | C | T | 89.40% | 0.00% | C -> T |
LOC_Os04g50188.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 52.612; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 |
|
vg0429946139 (J) | chr04 | 29946139 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os04g50188.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 51.909; most accessible tissue: Zhenshan97 flag leaf, score: 67.310 |
vg0429946193 (J) | chr04 | 29946193 | G | A | 94.10% | 0.00% | G -> A |
mr1117 (Jap_All); LR P-value: 4.95E-06;
mr1745 (Jap_All); LR P-value: 2.79E-07; mr1117_2 (Jap_All); LR P-value: 3.21E-07; mr1119_2 (Jap_All); LR P-value: 9.54E-07; mr1240_2 (Jap_All); LR P-value: 2.15E-06; mr1496_2 (Jap_All); LR P-value: 6.27E-06; mr1519_2 (Jap_All); LR P-value: 9.91E-06; mr1745_2 (Jap_All); LR P-value: 5.47E-06 |
LOC_Os04g50188.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 53.763; most accessible tissue: Minghui63 root, score: 67.730 |
vg0429946245 (J) | chr04 | 29946245 | C | T | 89.40% | 0.00% | C -> T |
LOC_Os04g50188.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 59.717; most accessible tissue: Minghui63 root, score: 73.351 |