21 variations found. LOC_Os07g14660 (harpin-induced protein 1 domain containing protein; expressed), ranging from 8,358,587 bp to 8,359,205 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0708358657 (J) | chr07 | 8358657 | C | T | 95.70% | 0.00% | C -> T | NA |
LOC_Os07g14660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 65.390; most accessible tissue: Zhenshan97 young leaf, score: 81.600 |
| vg0708358679 (J) | chr07 | 8358679 | G | T | 99.70% | 0.00% | G -> T | NA |
LOC_Os07g14660.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os07g14650.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g14670.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g14680.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g14650.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 70.666; most accessible tissue: Zhenshan97 young leaf, score: 81.841 |
| vg0708358798 (J) | chr07 | 8358798 | G | A | 97.50% | 0.00% | G -> A | NA |
LOC_Os07g14660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.962; most accessible tissue: Zhenshan97 young leaf, score: 82.077 |
| vg0708358828 (J) | chr07 | 8358828 | C | G | 97.50% | 0.00% | C -> G | NA |
LOC_Os07g14660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 75.570; most accessible tissue: Minghui63 young leaf, score: 82.907 |
| vg0708358947 (J) | chr07 | 8358947 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os07g14660.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g14650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g14670.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g14680.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g14650.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.851; most accessible tissue: Minghui63 flag leaf, score: 84.420 |
| vg0708358992 (J) | chr07 | 8358992 | C | T | 97.40% | 0.00% | C -> T | NA |
LOC_Os07g14660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 80.215; most accessible tissue: Minghui63 flag leaf, score: 85.836 |
| vg0708358997 (J) | chr07 | 8358997 | T | G | 97.50% | 0.00% | T -> G | NA |
LOC_Os07g14660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 80.125; most accessible tissue: Minghui63 flag leaf, score: 86.159 |
| vg0708359023 (J) | chr07 | 8359023 | C | T | 99.10% | 0.00% | C -> T | NA |
LOC_Os07g14660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.604; most accessible tissue: Minghui63 flag leaf, score: 85.151 |
| vg0708359027 (J) | chr07 | 8359027 | G | A | 99.70% | 0.00% | G -> A,T | NA |
LOC_Os07g14660.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os07g14650.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g14670.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g14680.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g14650.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g14660.1 Alt: T| missense_variant MODERATE(snpEff) LOC_Os07g14650.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g14670.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g14680.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g14650.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.562; most accessible tissue: Minghui63 young leaf, score: 85.028 |
| vg0708359028 (J) | chr07 | 8359028 | C | A | 97.50% | 0.00% | C -> A | NA |
LOC_Os07g14660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 79.580; most accessible tissue: Minghui63 young leaf, score: 85.028 |
| vg0708359031 (J) | chr07 | 8359031 | C | A | 97.50% | 0.00% | C -> A | NA |
LOC_Os07g14660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 79.380; most accessible tissue: Minghui63 young leaf, score: 85.028 |
| vg0708359079 (J) | chr07 | 8359079 | T | A | 97.50% | 0.00% | T -> A | NA |
LOC_Os07g14660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.771; most accessible tissue: Minghui63 young leaf, score: 84.814 |
| vg0708359116 (J) | chr07 | 8359116 | C | G | 54.20% | 0.00% | G -> C |
mr1037 (All); LR P-value: 1.94E-26;
mr1065 (All); LR P-value: 9.78E-58; mr1067 (All); LR P-value: 2.37E-44; mr1068 (All); LR P-value: 1.21E-57; mr1076 (All); LR P-value: 1.51E-27; mr1078 (All); LR P-value: 5.16E-52; mr1083 (All); LR P-value: 1.73E-22; mr1085 (All); LR P-value: 3.34E-31; mr1087 (All); LR P-value: 6.73E-58; mr1088 (All); LR P-value: 1.95E-60; mr1090 (All); LR P-value: 6.31E-54; mr1096 (All); LR P-value: 5.40E-50; mr1103 (All); LR P-value: 3.36E-56; mr1104 (All); LR P-value: 9.61E-34; mr1108 (All); LR P-value: 5.08E-46; mr1110 (All); LR P-value: 4.51E-35; mr1111 (All); LR P-value: 3.50E-48; mr1112 (All); LR P-value: 2.56E-47; mr1121 (All); LR P-value: 8.18E-49; mr1131 (All); LR P-value: 5.72E-20; mr1139 (All); LR P-value: 6.36E-42; mr1144 (All); LR P-value: 1.96E-44; mr1145 (All); LR P-value: 1.27E-28; mr1147 (All); LR P-value: 2.08E-16; mr1199 (All); LR P-value: 9.04E-15; mr1200 (All); LR P-value: 1.68E-44; mr1204 (All); LR P-value: 1.95E-31; mr1211 (All); LR P-value: 1.46E-51; mr1224 (All); LR P-value: 2.29E-31; mr1225 (All); LR P-value: 4.25E-31; mr1226 (All); LR P-value: 1.90E-31; mr1234 (All); LR P-value: 1.07E-47; mr1246 (All); LR P-value: 7.35E-61; mr1264 (All); LR P-value: 3.34E-26; mr1270 (All); LR P-value: 4.03E-13; mr1329 (All); LR P-value: 3.54E-12; mr1411 (All); LR P-value: 3.92E-26; mr1416 (All); LR P-value: 5.74E-22; mr1426 (All); LR P-value: 2.93E-27; mr1436 (All); LR P-value: 5.98E-30; mr1437 (All); LR P-value: 8.93E-44; mr1458 (All); LR P-value: 3.02E-41; mr1526 (All); LR P-value: 1.25E-47; mr1560 (All); LR P-value: 5.25E-31; mr1620 (All); LR P-value: 2.69E-39; mr1655 (All); LR P-value: 1.04E-12; mr1657 (All); LR P-value: 4.53E-11; mr1671 (All); LR P-value: 3.07E-59; mr1745 (All); LR P-value: 2.56E-32; mr1793 (All); LR P-value: 2.08E-28; mr1798 (All); LR P-value: 1.13E-51; mr1938 (All); LR P-value: 4.80E-13; mr1970 (All); LR P-value: 6.65E-64; mr1973 (All); LR P-value: 8.18E-81; mr1065_2 (All); LR P-value: 7.23E-69; mr1067_2 (All); LR P-value: 3.28E-61; mr1068_2 (All); LR P-value: 7.80E-71; mr1070_2 (All); LR P-value: 1.04E-45; mr1078_2 (All); LR P-value: 2.97E-65; mr1083_2 (All); LR P-value: 6.15E-33; mr1087_2 (All); LR P-value: 2.07E-71; mr1088_2 (All); LR P-value: 7.20E-77; mr1090_2 (All); LR P-value: 8.95E-64; mr1091_2 (All); LR P-value: 1.79E-49; mr1094_2 (All); LR P-value: 5.79E-45; mr1096_2 (All); LR P-value: 8.35E-60; mr1108_2 (All); LR P-value: 1.56E-59; mr1109_2 (All); LR P-value: 2.79E-55; mr1110_2 (All); LR P-value: 1.52E-40; mr1111_2 (All); LR P-value: 1.07E-53; mr1112_2 (All); LR P-value: 1.50E-67; mr1121_2 (All); LR P-value: 2.28E-54; mr1131_2 (All); LR P-value: 5.21E-18; mr1144_2 (All); LR P-value: 1.65E-55; mr1145_2 (All); LR P-value: 5.34E-42; mr1147_2 (All); LR P-value: 8.94E-13; mr1164_2 (All); LR P-value: 1.02E-21; mr1200_2 (All); LR P-value: 4.07E-58; mr1211_2 (All); LR P-value: 2.64E-55; mr1226_2 (All); LR P-value: 1.90E-39; mr1234_2 (All); LR P-value: 4.82E-61; mr1244_2 (All); LR P-value: 4.75E-26; mr1270_2 (All); LR P-value: 1.27E-29; mr1316_2 (All); LR P-value: 1.30E-23; mr1325_2 (All); LR P-value: 2.68E-13; mr1326_2 (All); LR P-value: 7.54E-14; mr1437_2 (All); LR P-value: 3.06E-45; mr1458_2 (All); LR P-value: 1.00E-48; mr1509_2 (All); LR P-value: 2.58E-44; mr1526_2 (All); LR P-value: 8.15E-61; mr1649_2 (All); LR P-value: 1.69E-09; mr1690_2 (All); LR P-value: 3.06E-08; mr1744_2 (All); LR P-value: 8.90E-16; mr1745_2 (All); LR P-value: 6.85E-39; mr1793_2 (All); LR P-value: 3.45E-45; mr1798_2 (All); LR P-value: 1.44E-67; mr1932_2 (All); LR P-value: 1.17E-30; mr1973_2 (All); LR P-value: 2.99E-95 |
LOC_Os07g14660.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 76.936; most accessible tissue: Minghui63 young leaf, score: 85.826 |
| vg0708359130 (J) | chr07 | 8359130 | T | C | 97.50% | 0.00% | T -> C | NA |
LOC_Os07g14660.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 77.579; most accessible tissue: Zhenshan97 young leaf, score: 85.715 |
| vg0708359134 (J) | chr07 | 8359134 | A | G | 97.50% | 0.00% | A -> G | NA |
LOC_Os07g14660.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.956; most accessible tissue: Zhenshan97 young leaf, score: 85.542 |
| vg0708359167 (J) | chr07 | 8359167 | A | C | 97.50% | 0.00% | A -> C | NA |
LOC_Os07g14660.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 77.537; most accessible tissue: Zhenshan97 young leaf, score: 87.004 |
| vg0708359170 (J) | chr07 | 8359170 | G | GGC | 97.60% | 0.00% | G -> GGC | NA |
LOC_Os07g14660.1 Alt: GGC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 77.422; most accessible tissue: Zhenshan97 young leaf, score: 86.852 |
| vg0708359171 (J) | chr07 | 8359171 | T | TGAGG | 97.50% | 0.00% | T -> TGAGG | NA |
LOC_Os07g14660.1 Alt: TGAGG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 77.422; most accessible tissue: Zhenshan97 young leaf, score: 86.852 |
| vg0708359172 (J) | chr07 | 8359172 | T | C | 97.50% | 0.00% | T -> C | NA |
LOC_Os07g14660.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 77.422; most accessible tissue: Zhenshan97 young leaf, score: 86.852 |
| vg0708359178 (J) | chr07 | 8359178 | T | A | 97.50% | 0.00% | T -> A | NA |
LOC_Os07g14660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 79.430; most accessible tissue: Zhenshan97 young leaf, score: 86.698 |
| vg0708359184 (J) | chr07 | 8359184 | T | G | 97.50% | 0.00% | T -> G | NA |
LOC_Os07g14660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 80.074; most accessible tissue: Zhenshan97 young leaf, score: 87.723 |