17 variations found. LOC_Os04g41759 (expressed protein), ranging from 24,746,953 bp to 24,748,506 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0424747103 (J) | chr04 | 24747103 | C | T | 98.70% | 0.00% | C -> T | NA |
LOC_Os04g41759.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.040; most accessible tissue: Minghui63 panicle, score: 90.408 |
| vg0424747105 (J) | chr04 | 24747105 | C | A | 90.10% | 0.00% | C -> A | NA |
LOC_Os04g41759.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 81.953; most accessible tissue: Minghui63 panicle, score: 90.408 |
| vg0424747125 (J) | chr04 | 24747125 | A | G | 59.70% | 0.59% | G -> A |
mr1509 (All); LR P-value: 2.14E-42;
mr1571 (All); LR P-value: 1.77E-23; mr1580 (All); LR P-value: 3.05E-21; mr1825 (All); LR P-value: 3.49E-18; mr1329_2 (All); LR P-value: 8.85E-06; mr1524_2 (All); LR P-value: 4.63E-06; mr1559_2 (All); LR P-value: 3.11E-06; mr1578_2 (All); LR P-value: 3.44E-15; mr1580_2 (All); LR P-value: 3.49E-30; mr1666_2 (All); LR P-value: 6.34E-12; mr1825_2 (All); LR P-value: 8.55E-29 |
LOC_Os04g41759.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41759.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 81.633; most accessible tissue: Minghui63 panicle, score: 89.175 |
| vg0424747239 (J) | chr04 | 24747239 | T | C | 92.70% | 0.00% | T -> C | NA |
LOC_Os04g41770.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41740.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41759.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.072; most accessible tissue: Minghui63 panicle, score: 89.175 |
| vg0424747359 (J) | chr04 | 24747359 | C | T | 59.90% | 0.63% | T -> C |
mr1379 (All); LR P-value: 1.51E-09;
mr1509 (All); LR P-value: 1.02E-41; mr1571 (All); LR P-value: 1.36E-23; mr1580 (All); LR P-value: 6.73E-22; mr1825 (All); LR P-value: 5.08E-19; mr1524_2 (All); LR P-value: 6.99E-06; mr1559_2 (All); LR P-value: 2.38E-06; mr1578_2 (All); LR P-value: 5.37E-15; mr1580_2 (All); LR P-value: 3.83E-30; mr1666_2 (All); LR P-value: 5.47E-12; mr1698_2 (All); LR P-value: 3.77E-21; mr1825_2 (All); LR P-value: 2.00E-29 |
LOC_Os04g41759.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os04g41759.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 79.164; most accessible tissue: Zhenshan97 flower, score: 87.550 |
| vg0424747477 (J) | chr04 | 24747477 | T | C | 52.50% | 0.55% | C -> T |
mr1026 (All); LR P-value: 1.90E-33;
mr1063 (All); LR P-value: 8.10E-53; mr1125 (All); LR P-value: 2.96E-48; mr1161 (All); LR P-value: 7.91E-34; mr1260 (All); LR P-value: 3.99E-09; mr1261 (All); LR P-value: 1.88E-16; mr1531 (All); LR P-value: 2.46E-13; mr1571 (All); LR P-value: 7.22E-23; mr1914 (All); LR P-value: 2.99E-12; mr1037_2 (All); LR P-value: 1.55E-30; mr1096_2 (All); LR P-value: 3.79E-59; mr1109_2 (All); LR P-value: 6.96E-56; mr1111_2 (All); LR P-value: 9.36E-51; mr1121_2 (All); LR P-value: 4.20E-52; mr1125_2 (All); LR P-value: 1.27E-65; mr1129_2 (All); LR P-value: 1.58E-36; mr1144_2 (All); LR P-value: 1.47E-53; mr1244_2 (All); LR P-value: 1.08E-24; mr1255_2 (All); LR P-value: 5.91E-21; mr1457_2 (All); LR P-value: 5.68E-17; mr1514_2 (All); LR P-value: 6.06E-13; mr1524_2 (All); LR P-value: 5.84E-06; mr1551_2 (All); LR P-value: 7.38E-23; mr1578_2 (All); LR P-value: 4.55E-15; mr1690_2 (All); LR P-value: 3.82E-08; mr1744_2 (All); LR P-value: 4.64E-16; mr1745_2 (All); LR P-value: 9.89E-41; mr1798_2 (All); LR P-value: 2.57E-73; mr1913_2 (All); LR P-value: 3.40E-32; mr1932_2 (All); LR P-value: 1.55E-29 |
LOC_Os04g41759.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41759.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 83.750; most accessible tissue: Zhenshan97 flower, score: 89.772 |
| vg0424747565 (J) | chr04 | 24747565 | G | A | 59.90% | 0.61% | A -> G |
mr1379 (All); LR P-value: 1.38E-09;
mr1509 (All); LR P-value: 6.58E-42; mr1571 (All); LR P-value: 7.02E-24; mr1580 (All); LR P-value: 9.52E-22; mr1731 (All); LR P-value: 1.20E-24; mr1825 (All); LR P-value: 5.54E-19; mr1524_2 (All); LR P-value: 5.87E-06; mr1559_2 (All); LR P-value: 3.03E-06; mr1578_2 (All); LR P-value: 2.97E-15; mr1580_2 (All); LR P-value: 3.32E-30; mr1666_2 (All); LR P-value: 4.41E-12; mr1698_2 (All); LR P-value: 2.34E-21; mr1825_2 (All); LR P-value: 4.35E-29 |
LOC_Os04g41759.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41759.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 82.934; most accessible tissue: Zhenshan97 flower, score: 89.027 |
| vg0424747759 (J) | chr04 | 24747759 | G | T | 59.80% | 0.66% | T -> G |
mr1379 (All); LR P-value: 1.53E-09;
mr1509 (All); LR P-value: 2.04E-41; mr1571 (All); LR P-value: 7.21E-24; mr1580 (All); LR P-value: 1.55E-21; mr1731 (All); LR P-value: 2.00E-24; mr1825 (All); LR P-value: 4.50E-19; mr1940 (All); LR P-value: 8.15E-12; mr1524_2 (All); LR P-value: 8.35E-06; mr1578_2 (All); LR P-value: 8.13E-15; mr1580_2 (All); LR P-value: 5.50E-30; mr1666_2 (All); LR P-value: 2.57E-12; mr1698_2 (All); LR P-value: 2.31E-21; mr1825_2 (All); LR P-value: 9.31E-29 |
LOC_Os04g41759.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41759.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 79.184; most accessible tissue: Minghui63 panicle, score: 88.281 |
| vg0424747761 (J) | chr04 | 24747761 | G | C | 59.80% | 0.66% | C -> G |
mr1379 (All); LR P-value: 1.38E-09;
mr1509 (All); LR P-value: 6.58E-42; mr1571 (All); LR P-value: 7.02E-24; mr1580 (All); LR P-value: 9.52E-22; mr1731 (All); LR P-value: 1.20E-24; mr1825 (All); LR P-value: 5.54E-19; mr1524_2 (All); LR P-value: 5.87E-06; mr1559_2 (All); LR P-value: 3.03E-06; mr1578_2 (All); LR P-value: 2.97E-15; mr1580_2 (All); LR P-value: 3.32E-30; mr1666_2 (All); LR P-value: 4.41E-12; mr1698_2 (All); LR P-value: 2.34E-21; mr1825_2 (All); LR P-value: 4.35E-29 |
LOC_Os04g41759.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41759.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 79.060; most accessible tissue: Minghui63 panicle, score: 88.281 |
| vg0424747815 (J) | chr04 | 24747815 | G | A | 59.80% | 0.59% | A -> G |
mr1379 (All); LR P-value: 1.38E-09;
mr1509 (All); LR P-value: 6.58E-42; mr1571 (All); LR P-value: 7.02E-24; mr1580 (All); LR P-value: 9.52E-22; mr1731 (All); LR P-value: 1.20E-24; mr1825 (All); LR P-value: 5.54E-19; mr1524_2 (All); LR P-value: 5.87E-06; mr1559_2 (All); LR P-value: 3.03E-06; mr1578_2 (All); LR P-value: 2.97E-15; mr1580_2 (All); LR P-value: 3.32E-30; mr1666_2 (All); LR P-value: 4.41E-12; mr1698_2 (All); LR P-value: 2.34E-21; mr1825_2 (All); LR P-value: 4.35E-29 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g41770.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41750.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41759.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.926; most accessible tissue: Minghui63 panicle, score: 87.605 |
| vg0424747863 (J) | chr04 | 24747863 | A | G | 88.70% | 0.00% | A -> G |
Plant_height (All); LR P-value: 7.74E-22;
Plant_height (Ind_All); LR P-value: 2.33E-15; mr1030 (All); LR P-value: 1.88E-07; mr1035 (Ind_All); LR P-value: 1.33E-06; mr1057 (All); LR P-value: 9.21E-07; mr1169 (All); LR P-value: 5.13E-12; mr1169 (Ind_All); LR P-value: 1.35E-06; mr1174 (All); LR P-value: 5.44E-10; mr1324 (Ind_All); LR P-value: 2.62E-06; mr1335 (Ind_All); LR P-value: 8.44E-06; mr1354 (Ind_All); LR P-value: 3.92E-06; mr1502 (Ind_All); LR P-value: 1.40E-06; mr1535 (Ind_All); LR P-value: 2.91E-08; mr1536 (Ind_All); LR P-value: 1.99E-06; mr1542 (Ind_All); LR P-value: 3.19E-06; mr1565 (All); LR P-value: 5.59E-10; mr1621 (All); LR P-value: 6.70E-06; mr1626 (Ind_All); LR P-value: 5.50E-06; mr1666 (All); LR P-value: 9.62E-08; mr1709 (All); LR P-value: 4.76E-08; mr1709 (Ind_All); LR P-value: 8.74E-07; mr1720 (All); LR P-value: 1.77E-10; mr1733 (Ind_All); LR P-value: 2.07E-06; mr1798 (Ind_All); LR P-value: 4.81E-06; mr1888 (Ind_All); LR P-value: 4.43E-06; mr1974 (All); LR P-value: 4.51E-06; mr1062_2 (Ind_All); LR P-value: 1.10E-06; mr1174_2 (All); LR P-value: 2.39E-09; mr1186_2 (All); LR P-value: 8.10E-06; mr1319_2 (All); LR P-value: 3.14E-10; mr1327_2 (All); LR P-value: 1.32E-09; mr1428_2 (All); LR P-value: 6.77E-06; mr1497_2 (All); LR P-value: 8.10E-06; mr1508_2 (All); LR P-value: 8.54E-06; mr1565_2 (All); LR P-value: 7.80E-11; mr1715_2 (Ind_All); LR P-value: 2.98E-11; mr1931_2 (All); LR P-value: 7.16E-07; mr1931_2 (Ind_All); LR P-value: 5.78E-07; mr1942_2 (Ind_All); LR P-value: 1.34E-06 |
LOC_Os04g41759.1 Alt: G| splice_acceptor_variant&intron_variant HIGH(snpEff)/splice_acceptor_variant(CooVar)
The average chromatin accessibility score: 76.272; most accessible tissue: Zhenshan97 panicle, score: 88.062 |
| vg0424747969 (J) | chr04 | 24747969 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os04g41759.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os04g41770.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g41750.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.229; most accessible tissue: Zhenshan97 panicle, score: 91.845 |
| vg0424747972 (J) | chr04 | 24747972 | C | A | 99.70% | 0.00% | C -> A | NA |
LOC_Os04g41759.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os04g41770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g41750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.333; most accessible tissue: Zhenshan97 panicle, score: 91.845 |
| vg0424748024 (J) | chr04 | 24748024 | C | T | 97.70% | 0.00% | C -> T | NA |
LOC_Os04g41759.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 81.967; most accessible tissue: Zhenshan97 panicle, score: 93.455 |
| vg0424748069 (J) | chr04 | 24748069 | C | T | 95.40% | 0.00% | C -> T | NA |
LOC_Os04g41759.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 83.593; most accessible tissue: Zhenshan97 panicle, score: 94.518 |
| vg0424748214 (J) | chr04 | 24748214 | A | G | 52.40% | 0.61% | G -> A |
mr1026 (All); LR P-value: 3.02E-33;
mr1063 (All); LR P-value: 9.09E-53; mr1125 (All); LR P-value: 1.97E-48; mr1161 (All); LR P-value: 1.21E-33; mr1221 (All); LR P-value: 6.14E-28; mr1260 (All); LR P-value: 5.92E-09; mr1261 (All); LR P-value: 3.30E-16; mr1531 (All); LR P-value: 3.79E-13; mr1745 (All); LR P-value: 7.44E-31; mr1914 (All); LR P-value: 4.05E-12; mr1037_2 (All); LR P-value: 1.10E-30; mr1094_2 (All); LR P-value: 3.67E-44; mr1096_2 (All); LR P-value: 1.38E-59; mr1109_2 (All); LR P-value: 8.42E-56; mr1111_2 (All); LR P-value: 7.07E-51; mr1121_2 (All); LR P-value: 1.24E-52; mr1125_2 (All); LR P-value: 1.64E-65; mr1129_2 (All); LR P-value: 1.98E-36; mr1144_2 (All); LR P-value: 1.01E-53; mr1208_2 (All); LR P-value: 2.30E-36; mr1244_2 (All); LR P-value: 7.72E-25; mr1255_2 (All); LR P-value: 9.90E-21; mr1270_2 (All); LR P-value: 1.08E-26; mr1457_2 (All); LR P-value: 5.90E-17; mr1514_2 (All); LR P-value: 6.89E-13; mr1524_2 (All); LR P-value: 9.91E-06; mr1551_2 (All); LR P-value: 1.59E-22; mr1578_2 (All); LR P-value: 4.57E-15; mr1690_2 (All); LR P-value: 5.29E-08; mr1744_2 (All); LR P-value: 4.35E-16; mr1745_2 (All); LR P-value: 5.87E-41; mr1798_2 (All); LR P-value: 1.37E-73; mr1913_2 (All); LR P-value: 2.66E-32; mr1932_2 (All); LR P-value: 8.46E-30 |
LOC_Os04g41759.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g41759.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 87.314; most accessible tissue: Callus, score: 96.371 |
| STR0424747099 (J) | chr04 | 24747099 | TCGGCTC GGCTGCT CG | TCGGCTA GGCTGCT CG | 80.60% | 0.00% | TCGGCTCGGC TGCTCG -> TCGGCTAGGC TGCTCG | NA |
|