27 variations found. LOC_Os06g41830 (SMP-30%2FGluconolaconase%2FLRE-like region containing protein; expressed), ranging from 25,085,536 bp to 25,086,526 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 |
---|---|---|---|---|---|---|---|---|---|
vg0625085588 (J) | chr06 | 25085588 | C | G | 57.00% | 0.00% | G -> C |
mr1047 (All); LR P-value: 8.93E-09;
mr1064 (All); LR P-value: 7.04E-39; mr1077 (All); LR P-value: 7.17E-19; mr1151 (All); LR P-value: 2.25E-09; mr1226 (All); LR P-value: 2.97E-29; mr1246 (All); LR P-value: 1.60E-61; mr1249 (All); LR P-value: 1.36E-07; mr1534 (All); LR P-value: 3.86E-44; mr1560 (All); LR P-value: 1.12E-29; mr1793 (All); LR P-value: 1.99E-28; mr1878 (All); LR P-value: 3.07E-32; mr1973 (All); LR P-value: 1.55E-80; mr1064_2 (All); LR P-value: 3.80E-59; mr1088_2 (All); LR P-value: 6.21E-75; mr1108_2 (All); LR P-value: 4.50E-54; mr1112_2 (All); LR P-value: 2.30E-61; mr1154_2 (All); LR P-value: 4.99E-50; mr1226_2 (All); LR P-value: 6.53E-39; mr1234_2 (All); LR P-value: 4.18E-58; mr1270_2 (All); LR P-value: 3.14E-27; mr1323_2 (All); LR P-value: 4.80E-27; mr1325_2 (All); LR P-value: 5.62E-13; mr1531_2 (All); LR P-value: 2.30E-19; mr1548_2 (All); LR P-value: 5.40E-07; mr1571_2 (All); LR P-value: 2.53E-33; mr1623_2 (All); LR P-value: 6.29E-07; mr1686_2 (All); LR P-value: 6.98E-15; mr1734_2 (All); LR P-value: 1.10E-10; mr1744_2 (All); LR P-value: 3.19E-16; mr1782_2 (All); LR P-value: 5.86E-11; mr1878_2 (All); LR P-value: 2.52E-35 |
LOC_Os06g41830.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.395; most accessible tissue: Zhenshan97 flag leaf, score: 92.451 |
vg0625085614 (J) | chr06 | 25085614 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os06g41830.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.979; most accessible tissue: Zhenshan97 flag leaf, score: 92.654 |
vg0625085615 (J) | chr06 | 25085615 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os06g41830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.192; most accessible tissue: Zhenshan97 flag leaf, score: 92.909 |
vg0625085617 (J) | chr06 | 25085617 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os06g41830.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.160; most accessible tissue: Zhenshan97 flag leaf, score: 92.909 |
vg0625085618 (J) | chr06 | 25085618 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os06g41830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.160; most accessible tissue: Zhenshan97 flag leaf, score: 92.909 |
vg0625085709 (J) | chr06 | 25085709 | T | C | 98.90% | 0.00% | T -> C | NA |
LOC_Os06g41830.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 87.354; most accessible tissue: Zhenshan97 flag leaf, score: 92.620 |
vg0625085827 (J) | chr06 | 25085827 | A | C | 64.10% | 0.00% | C -> A |
mr1028 (All); LR P-value: 1.87E-06;
mr1072 (All); LR P-value: 1.29E-26; mr1075 (All); LR P-value: 1.41E-28; mr1124 (All); LR P-value: 1.29E-41; mr1190 (All); LR P-value: 1.23E-07; mr1245 (All); LR P-value: 5.19E-07; mr1254 (All); LR P-value: 3.44E-21; mr1256 (All); LR P-value: 5.02E-30; mr1276 (All); LR P-value: 3.17E-16; mr1369 (All); LR P-value: 4.88E-07; mr1776 (All); LR P-value: 2.18E-08; mr1886 (All); LR P-value: 3.45E-07; mr1979 (All); LR P-value: 3.94E-07; mr1072_2 (All); LR P-value: 1.10E-37; mr1075_2 (All); LR P-value: 2.00E-37; mr1124_2 (All); LR P-value: 1.45E-57; mr1600_2 (All); LR P-value: 2.01E-08 |
LOC_Os06g41830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 80.441; most accessible tissue: Zhenshan97 flag leaf, score: 90.842 |
vg0625085860 (J) | chr06 | 25085860 | C | T | 84.20% | 0.00% | T -> C |
Grain_length (All); LR P-value: 5.49E-14;
Grain_length (Jap_All); LR P-value: 5.64E-14; mr1712 (All); LR P-value: 2.37E-11; mr1446_2 (All); LR P-value: 2.96E-07; mr1570_2 (Jap_All); LR P-value: 1.90E-07; mr1606_2 (All); LR P-value: 1.19E-07; mr1910_2 (All); LR P-value: 5.82E-06; mr1977_2 (All); LR P-value: 5.34E-06; mr1980_2 (All); LR P-value: 8.56E-18 |
LOC_Os06g41830.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.060; most accessible tissue: Minghui63 flag leaf, score: 90.430 |
vg0625085866 (J) | chr06 | 25085866 | C | A | 99.80% | 0.00% | C -> A | NA |
LOC_Os06g41830.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os06g41820.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.869; most accessible tissue: Minghui63 flag leaf, score: 90.261 |
vg0625085887 (J) | chr06 | 25085887 | G | A | 86.30% | 0.25% | G -> A | NA |
LOC_Os06g41830.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g41830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.088; most accessible tissue: Minghui63 flag leaf, score: 89.621 |
vg0625085896 (J) | chr06 | 25085896 | A | C | 70.90% | 0.00% | C -> A | NA |
LOC_Os06g41830.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.765; most accessible tissue: Minghui63 flag leaf, score: 89.016 |
vg0625085907 (J) | chr06 | 25085907 | T | A | 99.90% | 0.00% | T -> A | NA |
LOC_Os06g41830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 76.720; most accessible tissue: Minghui63 flag leaf, score: 88.223 |
vg0625085971 (J) | chr06 | 25085971 | T | A | 55.80% | 1.95% | A -> T |
mr1028 (All); LR P-value: 1.85E-06;
mr1072 (All); LR P-value: 6.51E-27; mr1075 (All); LR P-value: 5.53E-29; mr1124 (All); LR P-value: 1.54E-42; mr1190 (All); LR P-value: 1.41E-07; mr1202 (All); LR P-value: 7.69E-29; mr1245 (All); LR P-value: 4.34E-07; mr1254 (All); LR P-value: 2.01E-21; mr1256 (All); LR P-value: 1.55E-29; mr1276 (All); LR P-value: 2.97E-16; mr1369 (All); LR P-value: 5.04E-07; mr1660 (All); LR P-value: 8.51E-08; mr1690 (All); LR P-value: 8.48E-07; mr1776 (All); LR P-value: 2.13E-08; mr1861 (All); LR P-value: 2.53E-53; mr1886 (All); LR P-value: 3.44E-07; mr1962 (All); LR P-value: 1.50E-59; mr1979 (All); LR P-value: 2.92E-07; mr1072_2 (All); LR P-value: 2.36E-38; mr1075_2 (All); LR P-value: 3.39E-38; mr1124_2 (All); LR P-value: 9.10E-59; mr1276_2 (All); LR P-value: 4.80E-19; mr1600_2 (All); LR P-value: 1.75E-08; mr1861_2 (All); LR P-value: 1.89E-47 |
LOC_Os06g41830.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g41830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.551; most accessible tissue: Minghui63 flag leaf, score: 88.342 |
vg0625085973 (J) | chr06 | 25085973 | G | A | 84.60% | 10.28% | G -> A |
mr1123 (All); LR P-value: 4.01E-23;
mr1247 (All); LR P-value: 1.07E-21; mr1369 (All); LR P-value: 5.14E-07; mr1652 (All); LR P-value: 5.37E-07; mr1855 (All); LR P-value: 2.76E-21; mr1113_2 (All); LR P-value: 5.46E-17; mr1114_2 (All); LR P-value: 2.46E-16; mr1117_2 (All); LR P-value: 3.67E-19; mr1119_2 (All); LR P-value: 2.19E-17; mr1120_2 (All); LR P-value: 1.78E-22; mr1123_2 (All); LR P-value: 6.90E-24; mr1247_2 (All); LR P-value: 3.39E-24; mr1317_2 (All); LR P-value: 3.15E-09; mr1496_2 (All); LR P-value: 4.85E-13; mr1610_2 (All); LR P-value: 5.32E-11; mr1855_2 (All); LR P-value: 1.12E-24; mr1914_2 (All); LR P-value: 7.42E-13; mr1927_2 (All); LR P-value: 1.30E-16; mr1936_2 (All); LR P-value: 6.18E-15 |
LOC_Os06g41830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g41830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.188; most accessible tissue: Minghui63 flag leaf, score: 88.103 |
vg0625085974 (J) | chr06 | 25085974 | T | G | 55.90% | 1.95% | G -> T |
mr1028 (All); LMM P-value: 9.99E-07; LR P-value: 7.73E-07;
mr1072 (All); LR P-value: 1.24E-27; mr1075 (All); LR P-value: 3.43E-30; mr1124 (All); LR P-value: 5.28E-44; mr1190 (All); LR P-value: 7.37E-08; mr1202 (All); LR P-value: 1.66E-29; mr1245 (All); LR P-value: 2.13E-07; mr1254 (All); LR P-value: 8.44E-22; mr1256 (All); LR P-value: 4.84E-30; mr1276 (All); LR P-value: 1.93E-16; mr1369 (All); LMM P-value: 7.44E-06; LR P-value: 2.56E-07; mr1453 (All); LMM P-value: 2.47E-06; LR P-value: 4.87E-07; mr1776 (All); LR P-value: 1.54E-08; mr1861 (All); LR P-value: 9.43E-55; mr1886 (All); LR P-value: 3.29E-07; mr1962 (All); LR P-value: 4.47E-60; mr1979 (All); LR P-value: 3.60E-07; mr1072_2 (All); LR P-value: 5.44E-39; mr1075_2 (All); LR P-value: 6.02E-39; mr1124_2 (All); LR P-value: 2.03E-60; mr1148_2 (All); LR P-value: 5.23E-15; mr1276_2 (All); LR P-value: 4.77E-19; mr1600_2 (All); LR P-value: 2.59E-08; mr1861_2 (All); LR P-value: 1.47E-48 |
LOC_Os06g41830.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g41830.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os06g41830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.224; most accessible tissue: Minghui63 flag leaf, score: 88.103 |
vg0625085983 (J) | chr06 | 25085983 | C | A | 87.20% | 11.68% | C -> A | NA |
LOC_Os06g41830.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g41830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.324; most accessible tissue: Minghui63 flag leaf, score: 87.854 |
vg0625085998 (J) | chr06 | 25085998 | A | G | 86.60% | 0.00% | A -> G | NA |
LOC_Os06g41830.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.859; most accessible tissue: Minghui63 flag leaf, score: 87.854 |
vg0625086073 (J) | chr06 | 25086073 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os06g41830.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.604; most accessible tissue: Minghui63 panicle, score: 87.238 |
vg0625086218 (J) | chr06 | 25086218 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os06g41830.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os06g41820.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.4 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.011; most accessible tissue: Zhenshan97 root, score: 91.559 |
vg0625086220 (J) | chr06 | 25086220 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os06g41830.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os06g41820.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.4 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.123; most accessible tissue: Zhenshan97 root, score: 91.559 |
vg0625086222 (J) | chr06 | 25086222 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os06g41830.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os06g41820.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.4 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.036; most accessible tissue: Zhenshan97 root, score: 91.559 |
vg0625086356 (J) | chr06 | 25086356 | G | A | 98.90% | 0.00% | G -> A | NA |
LOC_Os06g41830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 83.403; most accessible tissue: Zhenshan97 root, score: 93.405 |
vg0625086439 (J) | chr06 | 25086439 | G | A | 98.90% | 0.00% | G -> A | NA |
LOC_Os06g41830.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 83.651; most accessible tissue: Zhenshan97 root, score: 92.725 |
vg0625086445 (J) | chr06 | 25086445 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os06g41830.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os06g41820.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os06g41840.4 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.548; most accessible tissue: Zhenshan97 root, score: 92.660 |
vg0625086447 (J) | chr06 | 25086447 | C | G | 99.90% | 0.00% | C -> G | NA |
LOC_Os06g41830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 83.548; most accessible tissue: Zhenshan97 root, score: 92.660 |
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