27 variations found. LOC_Os06g43170 (transposon protein; putative; unclassified; expressed), ranging from 25,945,634 bp to 25,949,545 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0625945636 (J) | chr06 | 25945636 | C | A | 97.40% | 0.00% | C -> A | NA |
LOC_Os06g43170.1 Alt: A| splice_region_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os06g43170.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g43150.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g43160.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.365; most accessible tissue: Callus, score: 94.847 |
| vg0625945804 (J) | chr06 | 25945804 | C | T | 97.40% | 0.00% | C -> T | NA |
LOC_Os06g43170.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g43150.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g43160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.073; most accessible tissue: Callus, score: 99.080 |
| vg0625945911 (J) | chr06 | 25945911 | A | G | 65.00% | 0.00% | G -> A |
mr1064 (All); LR P-value: 1.21E-36;
mr1072 (All); LR P-value: 3.48E-27; mr1074 (All); LR P-value: 3.55E-31; mr1081 (All); LR P-value: 5.68E-34; mr1092 (All); LR P-value: 1.09E-45; mr1124 (All); LR P-value: 3.19E-41; mr1130 (All); LR P-value: 9.27E-27; mr1148 (All); LR P-value: 2.49E-27; mr1152 (All); LR P-value: 4.63E-46; mr1154 (All); LR P-value: 3.22E-51; mr1202 (All); LR P-value: 2.19E-29; mr1245 (All); LR P-value: 1.04E-06; mr1254 (All); LR P-value: 3.53E-22; mr1256 (All); LR P-value: 6.60E-31; mr1439 (All); LR P-value: 1.52E-07; mr1534 (All); LR P-value: 3.85E-39; mr1571 (All); LR P-value: 9.57E-24; mr1776 (All); LR P-value: 1.18E-08; mr1824 (All); LR P-value: 4.25E-07; mr1861 (All); LR P-value: 2.29E-55; mr1886 (All); LR P-value: 1.07E-06; mr1922 (All); LR P-value: 2.16E-28; mr1924 (All); LR P-value: 8.26E-13; mr1940 (All); LR P-value: 2.17E-12; mr1979 (All); LR P-value: 5.64E-07; mr1064_2 (All); LR P-value: 3.96E-59; mr1072_2 (All); LR P-value: 2.94E-38; mr1074_2 (All); LR P-value: 1.14E-27; mr1075_2 (All); LR P-value: 2.61E-37; mr1081_2 (All); LR P-value: 2.96E-32; mr1124_2 (All); LR P-value: 1.17E-58; mr1148_2 (All); LR P-value: 3.92E-15; mr1256_2 (All); LR P-value: 1.72E-33; mr1861_2 (All); LR P-value: 1.09E-48 |
LOC_Os06g43170.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g43150.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g43160.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.485; most accessible tissue: Callus, score: 95.442 |
| vg0625945976 (J) | chr06 | 25945976 | G | C | 64.90% | 0.00% | C -> G |
mr1070 (All); LR P-value: 2.02E-10;
mr1072 (All); LR P-value: 1.38E-26; mr1074 (All); LR P-value: 2.33E-32; mr1081 (All); LR P-value: 1.86E-35; mr1092 (All); LR P-value: 3.70E-46; mr1097 (All); LR P-value: 3.15E-09; mr1124 (All); LR P-value: 1.35E-40; mr1130 (All); LR P-value: 2.76E-26; mr1148 (All); LR P-value: 6.35E-29; mr1152 (All); LR P-value: 3.48E-46; mr1154 (All); LR P-value: 1.13E-52; mr1202 (All); LR P-value: 5.67E-29; mr1245 (All); LR P-value: 5.48E-07; mr1254 (All); LR P-value: 3.07E-23; mr1256 (All); LR P-value: 6.84E-32; mr1278 (All); LR P-value: 1.40E-06; mr1302 (All); LR P-value: 6.45E-09; mr1307 (All); LR P-value: 5.83E-10; mr1315 (All); LR P-value: 1.44E-06; mr1376 (All); LR P-value: 1.83E-14; mr1392 (All); LR P-value: 2.18E-06; mr1431 (All); LR P-value: 1.83E-14; mr1439 (All); LR P-value: 4.36E-08; mr1442 (All); LR P-value: 7.34E-09; mr1488 (All); LR P-value: 4.52E-08; mr1571 (All); LR P-value: 9.78E-25; mr1601 (All); LR P-value: 3.68E-37; mr1604 (All); LR P-value: 7.95E-08; mr1660 (All); LR P-value: 5.80E-08; mr1776 (All); LR P-value: 4.85E-09; mr1797 (All); LR P-value: 8.52E-07; mr1801 (All); LR P-value: 8.52E-07; mr1810 (All); LR P-value: 2.96E-07; mr1824 (All); LR P-value: 1.40E-07; mr1861 (All); LR P-value: 1.18E-54; mr1886 (All); LR P-value: 9.39E-07; mr1922 (All); LR P-value: 5.82E-29; mr1924 (All); LR P-value: 4.11E-13; mr1940 (All); LR P-value: 1.13E-12; mr1979 (All); LR P-value: 7.08E-07; mr1064_2 (All); LR P-value: 3.59E-59; mr1072_2 (All); LR P-value: 5.98E-38; mr1074_2 (All); LR P-value: 2.15E-28; mr1075_2 (All); LR P-value: 5.18E-37; mr1081_2 (All); LR P-value: 4.75E-33; mr1092_2 (All); LR P-value: 4.81E-40; mr1124_2 (All); LR P-value: 5.01E-59; mr1148_2 (All); LR P-value: 1.64E-15; mr1152_2 (All); LR P-value: 6.15E-40; mr1154_2 (All); LR P-value: 2.69E-50; mr1256_2 (All); LR P-value: 2.04E-34; mr1861_2 (All); LR P-value: 6.18E-49 |
LOC_Os06g43170.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g43150.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g43160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.425; most accessible tissue: Callus, score: 98.240 |
| vg0625946018 (J) | chr06 | 25946018 | G | A | 97.40% | 0.00% | G -> A | NA |
LOC_Os06g43170.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g43160.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.327; most accessible tissue: Callus, score: 98.240 |
| vg0625946080 (J) | chr06 | 25946080 | GAA | G | 65.80% | 0.00% | G -> GAA,A | NA |
LOC_Os06g43170.1 Alt: GAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g43160.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g43170.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g43160.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.263; most accessible tissue: Zhenshan97 panicle, score: 92.660 |
| vg0625946127 (J) | chr06 | 25946127 | GAA | G | 64.90% | 0.00% | G -> GAA | NA |
LOC_Os06g43170.1 Alt: GAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g43160.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.378; most accessible tissue: Zhenshan97 flower, score: 91.224 |
| vg0625946129 (J) | chr06 | 25946129 | G | A | 73.40% | 6.39% | G -> A | NA |
LOC_Os06g43170.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g43160.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 84.153; most accessible tissue: Zhenshan97 flower, score: 91.191 |
| vg0625946301 (J) | chr06 | 25946301 | A | C | 62.10% | 0.00% | C -> A |
mr1064 (All); LR P-value: 5.12E-37;
mr1072 (All); LR P-value: 4.07E-27; mr1092 (All); LR P-value: 2.92E-45; mr1103 (All); LR P-value: 1.17E-55; mr1124 (All); LR P-value: 1.41E-41; mr1152 (All); LR P-value: 2.46E-43; mr1154 (All); LR P-value: 3.72E-50; mr1172 (All); LR P-value: 8.77E-11; mr1534 (All); LR P-value: 1.58E-40; mr1571 (All); LR P-value: 5.36E-24; mr1751 (All); LR P-value: 1.18E-10; mr1861 (All); LR P-value: 5.11E-57; mr1886 (All); LR P-value: 6.30E-07; mr1064_2 (All); LR P-value: 3.00E-60; mr1075_2 (All); LR P-value: 1.88E-36; mr1103_2 (All); LR P-value: 2.60E-67; mr1124_2 (All); LR P-value: 1.11E-59; mr1145_2 (All); LR P-value: 1.82E-41; mr1226_2 (All); LR P-value: 4.05E-38; mr1600_2 (All); LR P-value: 1.43E-08; mr1861_2 (All); LR P-value: 5.83E-49 |
LOC_Os06g43170.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g43160.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.558; most accessible tissue: Callus, score: 95.414 |
| vg0625946440 (J) | chr06 | 25946440 | G | C | 97.40% | 0.00% | G -> C | NA |
LOC_Os06g43170.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.765; most accessible tissue: Zhenshan97 flower, score: 92.719 |
| vg0625946442 (J) | chr06 | 25946442 | C | T | 62.20% | 0.00% | T -> C | NA |
LOC_Os06g43170.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 88.063; most accessible tissue: Zhenshan97 panicle, score: 93.020 |
| vg0625946542 (J) | chr06 | 25946542 | G | A | 97.40% | 0.00% | G -> A | NA |
LOC_Os06g43170.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.163; most accessible tissue: Zhenshan97 panicle, score: 95.493 |
| vg0625946809 (J) | chr06 | 25946809 | C | CGCGGCT | 61.90% | 0.00% | CGCGGCT -> C | NA |
LOC_Os06g43170.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 90.721; most accessible tissue: Zhenshan97 panicle, score: 95.903 |
| vg0625946815 (J) | chr06 | 25946815 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os06g43170.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os06g43160.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.694; most accessible tissue: Zhenshan97 panicle, score: 96.130 |
| vg0625946828 (J) | chr06 | 25946828 | A | G | 62.20% | 0.00% | G -> A |
mr1064 (All); LR P-value: 5.12E-37;
mr1072 (All); LR P-value: 4.07E-27; mr1092 (All); LR P-value: 2.92E-45; mr1103 (All); LR P-value: 1.17E-55; mr1124 (All); LR P-value: 1.41E-41; mr1152 (All); LR P-value: 2.46E-43; mr1154 (All); LR P-value: 3.72E-50; mr1172 (All); LR P-value: 8.77E-11; mr1534 (All); LR P-value: 1.58E-40; mr1571 (All); LR P-value: 5.36E-24; mr1751 (All); LR P-value: 1.18E-10; mr1861 (All); LR P-value: 5.11E-57; mr1886 (All); LR P-value: 6.30E-07; mr1064_2 (All); LR P-value: 3.00E-60; mr1075_2 (All); LR P-value: 1.88E-36; mr1103_2 (All); LR P-value: 2.60E-67; mr1124_2 (All); LR P-value: 1.11E-59; mr1145_2 (All); LR P-value: 1.82E-41; mr1226_2 (All); LR P-value: 4.05E-38; mr1600_2 (All); LR P-value: 1.43E-08; mr1861_2 (All); LR P-value: 5.83E-49 |
LOC_Os06g43170.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 88.536; most accessible tissue: Zhenshan97 panicle, score: 96.173 |
| vg0625947025 (J) | chr06 | 25947025 | A | C | 62.20% | 0.00% | C -> A |
mr1064 (All); LR P-value: 5.12E-37;
mr1072 (All); LR P-value: 4.07E-27; mr1092 (All); LR P-value: 2.92E-45; mr1103 (All); LR P-value: 1.17E-55; mr1124 (All); LR P-value: 1.41E-41; mr1152 (All); LR P-value: 2.46E-43; mr1154 (All); LR P-value: 3.72E-50; mr1172 (All); LR P-value: 8.77E-11; mr1534 (All); LR P-value: 1.58E-40; mr1571 (All); LR P-value: 5.36E-24; mr1751 (All); LR P-value: 1.18E-10; mr1861 (All); LR P-value: 5.11E-57; mr1886 (All); LR P-value: 6.30E-07; mr1064_2 (All); LR P-value: 3.00E-60; mr1075_2 (All); LR P-value: 1.88E-36; mr1103_2 (All); LR P-value: 2.60E-67; mr1124_2 (All); LR P-value: 1.11E-59; mr1145_2 (All); LR P-value: 1.82E-41; mr1226_2 (All); LR P-value: 4.05E-38; mr1600_2 (All); LR P-value: 1.43E-08; mr1861_2 (All); LR P-value: 5.83E-49 |
LOC_Os06g43170.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.131; most accessible tissue: Minghui63 panicle, score: 93.837 |
| vg0625947288 (J) | chr06 | 25947288 | T | A | 62.10% | 0.00% | A -> T |
mr1064 (All); LR P-value: 3.02E-37;
mr1072 (All); LR P-value: 2.51E-26; mr1092 (All); LR P-value: 5.13E-45; mr1103 (All); LR P-value: 2.40E-56; mr1124 (All); LR P-value: 1.25E-40; mr1152 (All); LR P-value: 2.64E-43; mr1154 (All); LR P-value: 1.66E-49; mr1172 (All); LR P-value: 3.81E-11; mr1534 (All); LR P-value: 1.63E-40; mr1571 (All); LR P-value: 1.88E-23; mr1861 (All); LR P-value: 3.16E-56; mr1886 (All); LR P-value: 1.09E-06; mr1064_2 (All); LR P-value: 6.76E-60; mr1085_2 (All); LR P-value: 1.76E-31; mr1103_2 (All); LR P-value: 6.55E-68; mr1124_2 (All); LR P-value: 1.61E-58; mr1145_2 (All); LR P-value: 3.77E-42; mr1226_2 (All); LR P-value: 3.50E-38; mr1264_2 (All); LR P-value: 8.06E-39; mr1600_2 (All); LR P-value: 2.35E-08; mr1623_2 (All); LR P-value: 5.18E-07; mr1686_2 (All); LR P-value: 8.73E-15; mr1861_2 (All); LR P-value: 2.35E-48 |
LOC_Os06g43160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g43170.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 81.233; most accessible tissue: Minghui63 panicle, score: 93.735 |
| vg0625947680 (J) | chr06 | 25947680 | G | A | 97.30% | 0.00% | G -> A | NA |
LOC_Os06g43170.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.668; most accessible tissue: Zhenshan97 panicle, score: 92.660 |
| vg0625947874 (J) | chr06 | 25947874 | G | C | 97.90% | 0.00% | G -> C | NA |
LOC_Os06g43170.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 78.688; most accessible tissue: Zhenshan97 panicle, score: 93.020 |
| vg0625948152 (J) | chr06 | 25948152 | A | C | 97.40% | 0.00% | A -> C | NA |
LOC_Os06g43170.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.915; most accessible tissue: Zhenshan97 panicle, score: 89.143 |
| vg0625948566 (J) | chr06 | 25948566 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os06g43170.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 83.438; most accessible tissue: Zhenshan97 panicle, score: 92.533 |
| vg0625948582 (J) | chr06 | 25948582 | A | G | 62.10% | 0.00% | G -> A |
mr1072 (All); LR P-value: 6.47E-27;
mr1092 (All); LR P-value: 1.93E-46; mr1124 (All); LR P-value: 2.83E-41; mr1152 (All); LR P-value: 3.03E-44; mr1154 (All); LR P-value: 4.79E-51; mr1172 (All); LR P-value: 1.27E-10; mr1534 (All); LR P-value: 3.45E-39; mr1571 (All); LR P-value: 9.57E-24; mr1604 (All); LR P-value: 2.47E-07; mr1861 (All); LR P-value: 2.31E-56; mr1886 (All); LR P-value: 3.31E-07; mr1064_2 (All); LR P-value: 1.58E-59; mr1124_2 (All); LR P-value: 5.38E-59; mr1600_2 (All); LR P-value: 2.16E-08; mr1861_2 (All); LR P-value: 9.80E-50 |
LOC_Os06g43170.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.242; most accessible tissue: Zhenshan97 panicle, score: 92.133 |
| vg0625948745 (J) | chr06 | 25948745 | G | A | 97.30% | 0.00% | G -> A | NA |
LOC_Os06g43170.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.732; most accessible tissue: Zhenshan97 panicle, score: 93.351 |
| vg0625949203 (J) | chr06 | 25949203 | T | C | 62.00% | 0.00% | C -> T |
mr1064 (All); LR P-value: 1.80E-36;
mr1072 (All); LR P-value: 1.85E-26; mr1092 (All); LR P-value: 6.25E-44; mr1124 (All); LR P-value: 5.68E-41; mr1172 (All); LR P-value: 9.86E-11; mr1534 (All); LR P-value: 4.83E-40; mr1571 (All); LR P-value: 6.21E-24; mr1861 (All); LR P-value: 2.15E-55; mr1886 (All); LR P-value: 7.30E-07; mr1064_2 (All); LR P-value: 1.21E-60; mr1103_2 (All); LR P-value: 1.18E-66; mr1124_2 (All); LR P-value: 1.05E-58; mr1145_2 (All); LR P-value: 2.24E-41; mr1600_2 (All); LR P-value: 1.23E-08; mr1861_2 (All); LR P-value: 5.66E-49 |
LOC_Os06g43170.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.631; most accessible tissue: Zhenshan97 panicle, score: 97.512 |
| vg0625949379 (J) | chr06 | 25949379 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os06g43170.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.925; most accessible tissue: Zhenshan97 panicle, score: 98.532 |
| vg0625949415 (J) | chr06 | 25949415 | C | G | 97.40% | 0.00% | C -> G | NA |
LOC_Os06g43170.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 93.742; most accessible tissue: Zhenshan97 panicle, score: 99.042 |
| STR0625946075 (J) | chr06 | 25946075 | AGAGA | AGA | 65.20% | 0.00% | AGA -> AGAGA | NA |
|