24 variations found. LOC_Os03g10910 (NB-ARC%2FLRR disease resistance protein; putative; expressed), ranging from 5,607,031 bp to 5,609,758 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0305607314 (J) | chr03 | 5607314 | TGCG | T | 94.20% | 0.00% | TGCG -> T | NA |
LOC_Os03g10910.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 90.926; most accessible tissue: Minghui63 flag leaf, score: 94.110 |
| vg0305607486 (J) | chr03 | 5607486 | C | T | 94.10% | 0.00% | C -> T |
LOC_Os03g10910.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.103; most accessible tissue: Minghui63 flag leaf, score: 94.147 |
|
| vg0305607504 (J) | chr03 | 5607504 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g10910.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g10920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.108; most accessible tissue: Minghui63 flag leaf, score: 94.329 |
| vg0305607802 (J) | chr03 | 5607802 | G | A | 96.30% | 0.00% | G -> A | NA |
LOC_Os03g10910.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.444; most accessible tissue: Zhenshan97 flag leaf, score: 92.620 |
| vg0305607901 (J) | chr03 | 5607901 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os03g10910.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g10920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.376; most accessible tissue: Zhenshan97 flag leaf, score: 92.089 |
| vg0305607955 (J) | chr03 | 5607955 | G | A | 98.00% | 0.00% | G -> A | NA |
LOC_Os03g10910.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.913; most accessible tissue: Zhenshan97 flower, score: 92.245 |
| vg0305608019 (J) | chr03 | 5608019 | G | C | 96.30% | 0.00% | G -> C | NA |
LOC_Os03g10910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.288; most accessible tissue: Zhenshan97 flower, score: 93.075 |
| vg0305608033 (J) | chr03 | 5608033 | C | T | 66.50% | 0.25% | T -> C | NA |
LOC_Os03g10910.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g10910.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.417; most accessible tissue: Zhenshan97 flower, score: 93.121 |
| vg0305608124 (J) | chr03 | 5608124 | T | A | 99.90% | 0.00% | T -> A,G | NA |
LOC_Os03g10910.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g10920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g10910.1 Alt: G| missense_variant MODERATE(snpEff) LOC_Os03g10920.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.092; most accessible tissue: Zhenshan97 flower, score: 94.410 |
| vg0305608657 (J) | chr03 | 5608657 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g10910.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g10920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g10930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g10930.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.163; most accessible tissue: Zhenshan97 flower, score: 95.508 |
| vg0305608726 (J) | chr03 | 5608726 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os03g10910.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g10920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g10930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g10930.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.335; most accessible tissue: Zhenshan97 flower, score: 95.496 |
| vg0305608789 (J) | chr03 | 5608789 | G | C | 66.30% | 0.25% | C -> G | NA |
LOC_Os03g10910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g10910.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 88.058; most accessible tissue: Zhenshan97 flower, score: 94.648 |
| vg0305608837 (J) | chr03 | 5608837 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os03g10910.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g10920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g10930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g10930.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.125; most accessible tissue: Zhenshan97 flower, score: 95.170 |
| vg0305608906 (J) | chr03 | 5608906 | G | T | 99.80% | 0.00% | G -> T | NA |
LOC_Os03g10910.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g10920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g10930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g10930.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.910; most accessible tissue: Zhenshan97 flower, score: 95.104 |
| vg0305608960 (J) | chr03 | 5608960 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os03g10910.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g10920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g10930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g10930.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.181; most accessible tissue: Zhenshan97 flower, score: 95.078 |
| vg0305609108 (J) | chr03 | 5609108 | G | T | 66.50% | 0.23% | T -> G | NA |
LOC_Os03g10910.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g10910.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 88.099; most accessible tissue: Zhenshan97 flower, score: 94.410 |
| vg0305609206 (J) | chr03 | 5609206 | C | T | 66.50% | 0.25% | T -> C | NA |
LOC_Os03g10910.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g10910.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 88.743; most accessible tissue: Zhenshan97 flower, score: 93.774 |
| vg0305609302 (J) | chr03 | 5609302 | C | T | 94.10% | 0.00% | C -> T |
LOC_Os03g10910.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.114; most accessible tissue: Zhenshan97 flower, score: 91.514 |
|
| vg0305609366 (J) | chr03 | 5609366 | A | C | 54.60% | 0.25% | C -> A |
mr1037 (All); LR P-value: 4.95E-27;
mr1065 (All); LR P-value: 1.46E-53; mr1068 (All); LR P-value: 2.08E-53; mr1083 (All); LR P-value: 1.00E-23; mr1088 (All); LR P-value: 2.23E-59; mr1090 (All); LR P-value: 2.05E-52; mr1108 (All); LR P-value: 1.09E-44; mr1111 (All); LR P-value: 8.23E-46; mr1112 (All); LR P-value: 7.76E-44; mr1139 (All); LR P-value: 1.69E-39; mr1144 (All); LR P-value: 3.64E-42; mr1147 (All); LR P-value: 5.75E-17; mr1200 (All); LR P-value: 1.22E-41; mr1204 (All); LR P-value: 1.01E-30; mr1225 (All); LR P-value: 4.81E-31; mr1234 (All); LR P-value: 2.05E-46; mr1237 (All); LR P-value: 2.41E-30; mr1264 (All); LR P-value: 1.48E-24; mr1404 (All); LR P-value: 4.69E-34; mr1411 (All); LR P-value: 6.30E-25; mr1436 (All); LR P-value: 1.39E-29; mr1531 (All); LR P-value: 7.39E-13; mr1551 (All); LR P-value: 2.31E-24; mr1560 (All); LR P-value: 4.81E-31; mr1620 (All); LR P-value: 1.13E-38; mr1655 (All); LR P-value: 3.74E-13; mr1671 (All); LR P-value: 1.16E-57; mr1717 (All); LR P-value: 3.32E-07; mr1721 (All); LR P-value: 4.71E-41; mr1770 (All); LR P-value: 1.47E-08; mr1798 (All); LR P-value: 4.17E-52; mr1878 (All); LR P-value: 3.79E-34; mr1946 (All); LR P-value: 5.67E-08; mr1973 (All); LR P-value: 1.54E-80; mr1065_2 (All); LR P-value: 1.00E-65; mr1068_2 (All); LR P-value: 3.10E-67; mr1078_2 (All); LR P-value: 6.85E-63; mr1090_2 (All); LR P-value: 7.52E-61; mr1091_2 (All); LR P-value: 5.00E-49; mr1094_2 (All); LR P-value: 2.39E-46; mr1096_2 (All); LR P-value: 1.50E-61; mr1108_2 (All); LR P-value: 7.58E-56; mr1111_2 (All); LR P-value: 1.02E-52; mr1112_2 (All); LR P-value: 2.10E-62; mr1144_2 (All); LR P-value: 5.75E-54; mr1147_2 (All); LR P-value: 2.08E-13; mr1161_2 (All); LR P-value: 1.00E-32; mr1200_2 (All); LR P-value: 3.54E-53; mr1234_2 (All); LR P-value: 3.31E-60; mr1244_2 (All); LR P-value: 2.34E-25; mr1509_2 (All); LR P-value: 8.63E-44; mr1531_2 (All); LR P-value: 5.87E-21; mr1571_2 (All); LR P-value: 2.83E-34; mr1793_2 (All); LR P-value: 1.77E-46; mr1798_2 (All); LR P-value: 6.71E-71; mr1807_2 (All); LR P-value: 1.41E-13; mr1913_2 (All); LR P-value: 5.11E-32; mr1973_2 (All); LR P-value: 2.27E-95 |
LOC_Os03g10910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g10910.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 84.513; most accessible tissue: Minghui63 flower, score: 90.757 |
| vg0305609404 (J) | chr03 | 5609404 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os03g10910.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g10920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g10930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g10930.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.698; most accessible tissue: Minghui63 flower, score: 90.103 |
| vg0305609550 (J) | chr03 | 5609550 | G | GCGA | 98.10% | 0.00% | G -> GCGA | NA |
LOC_Os03g10910.1 Alt: GCGA| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 81.116; most accessible tissue: Zhenshan97 root, score: 88.778 |
| vg0305609663 (J) | chr03 | 5609663 | C | T | 66.50% | 0.21% | T -> C | NA |
LOC_Os03g10910.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g10910.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 74.195; most accessible tissue: Zhenshan97 root, score: 88.318 |
| vg0305609714 (J) | chr03 | 5609714 | G | A | 96.40% | 0.00% | G -> A | NA |
LOC_Os03g10910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 74.381; most accessible tissue: Callus, score: 93.831 |
| STR0305607315 (J) | chr03 | 5607315 | GCGGCGG CGGCGGC G | GCGGCGG CGGCG | 95.90% | 0.00% | GCGGCGGCGG CGGCG -> GCGGCGGCGG CG | NA |
|