147 variations found. LOC_Os02g39660 (receptor kinase; putative; expressed), ranging from 23,952,925 bp to 23,954,617 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0223952968 (J) | chr02 | 23952968 | T | G | 82.30% | 15.47% | T -> G | NA |
LOC_Os02g39660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 79.026; most accessible tissue: Callus, score: 91.840 |
| vg0223952985 (J) | chr02 | 23952985 | C | T | 71.10% | 16.23% | C -> T | NA |
LOC_Os02g39660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 79.102; most accessible tissue: Callus, score: 91.840 |
| vg0223952991 (J) | chr02 | 23952991 | C | T | 69.20% | 16.17% | C -> T |
mr1067 (Ind_All); LR P-value: 2.58E-13;
mr1069 (Ind_All); LR P-value: 1.55E-06; mr1072 (Ind_All); LR P-value: 6.45E-06; mr1074 (Ind_All); LR P-value: 6.97E-08; mr1075 (Ind_All); LR P-value: 4.17E-06; mr1077 (Ind_All); LR P-value: 2.16E-08; mr1080 (Ind_All); LR P-value: 6.50E-06; mr1100 (Ind_All); LR P-value: 3.66E-07; mr1124 (Ind_All); LR P-value: 4.16E-06; mr1148 (Ind_All); LR P-value: 1.36E-07; mr1202 (Ind_All); LR P-value: 3.54E-06; mr1861 (Ind_All); LR P-value: 2.70E-10; mr1918 (Ind_All); LR P-value: 5.09E-06; mr1962 (Ind_All); LR P-value: 1.47E-09; mr1067_2 (Ind_All); LR P-value: 1.99E-14; mr1072_2 (Ind_All); LR P-value: 4.55E-08; mr1074_2 (Ind_All); LR P-value: 1.52E-07; mr1075_2 (Ind_All); LR P-value: 2.57E-08; mr1077_2 (Ind_All); LR P-value: 3.65E-08; mr1100_2 (Ind_All); LR P-value: 1.80E-08; mr1124_2 (Ind_All); LR P-value: 2.39E-10; mr1148_2 (Ind_All); LR P-value: 8.67E-06; mr1150_2 (Ind_All); LR P-value: 1.03E-06; mr1222_2 (All); LR P-value: 1.33E-12; mr1222_2 (Ind_All); LR P-value: 3.57E-09; mr1402_2 (Ind_All); LR P-value: 4.63E-06; mr1558_2 (Ind_All); LR P-value: 3.97E-06; mr1619_2 (Ind_All); LR P-value: 9.57E-07; mr1795_2 (Ind_All); LR P-value: 5.32E-07; mr1918_2 (Ind_All); LR P-value: 2.37E-07; mr1962_2 (Ind_All); LR P-value: 1.09E-11 |
LOC_Os02g39660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.798; most accessible tissue: Callus, score: 91.840 |
| vg0223952998 (J) | chr02 | 23952998 | G | A | 69.60% | 16.38% | G -> A |
LOC_Os02g39660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.664; most accessible tissue: Callus, score: 91.840 |
|
| vg0223953092 (J) | chr02 | 23953092 | C | T | 82.20% | 15.74% | C -> T | NA |
LOC_Os02g39660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 69.866; most accessible tissue: Zhenshan97 young leaf, score: 86.698 |
| vg0223953106 (J) | chr02 | 23953106 | C | T | 69.50% | 16.36% | C -> T |
mr1099 (Ind_All); LR P-value: 5.32E-06;
mr1101 (Ind_All); LR P-value: 3.89E-06; mr1334 (Ind_All); LR P-value: 4.36E-06; mr1861 (Ind_All); LR P-value: 2.68E-07; mr1868 (Ind_All); LR P-value: 1.90E-06; mr1072_2 (Ind_All); LMM P-value: 8.18E-06; LR P-value: 3.05E-09; mr1075_2 (Ind_All); LMM P-value: 9.98E-06; LR P-value: 3.69E-09; mr1149_2 (Ind_All); LR P-value: 3.76E-07; mr1150_2 (All); LMM P-value: 7.35E-06 |
LOC_Os02g39660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 69.919; most accessible tissue: Zhenshan97 young leaf, score: 86.698 |
| vg0223953113 (J) | chr02 | 23953113 | A | G | 82.20% | 15.74% | A -> G | NA |
LOC_Os02g39660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 69.183; most accessible tissue: Zhenshan97 young leaf, score: 86.383 |
| vg0223953133 (J) | chr02 | 23953133 | C | T | 80.80% | 16.08% | C -> T | NA |
LOC_Os02g39660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 68.797; most accessible tissue: Zhenshan97 young leaf, score: 86.383 |
| vg0223953241 (J) | chr02 | 23953241 | G | A | 81.80% | 15.93% | G -> A | NA |
LOC_Os02g39660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 66.930; most accessible tissue: Callus, score: 79.908 |
| vg0223953274 (J) | chr02 | 23953274 | AAC | A | 83.40% | 15.49% | AAC -> A | NA |
LOC_Os02g39660.1 Alt: A/frameshift_variant(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 65.773; most accessible tissue: Callus, score: 79.908 |
| vg0223953305 (J) | chr02 | 23953305 | T | A | 83.50% | 15.55% | T -> A | NA |
LOC_Os02g39660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 64.711; most accessible tissue: Callus, score: 79.908 |
| vg0223953316 (J) | chr02 | 23953316 | A | T | 68.20% | 15.68% | A -> T |
mr1099 (Ind_All); LR P-value: 4.34E-06;
mr1101 (Ind_All); LR P-value: 3.26E-06; mr1334 (Ind_All); LR P-value: 3.95E-06; mr1861 (Ind_All); LR P-value: 3.12E-07; mr1868 (Ind_All); LR P-value: 1.67E-06; mr1072_2 (Ind_All); LMM P-value: 7.45E-06; LR P-value: 2.57E-09; mr1075_2 (Ind_All); LMM P-value: 8.95E-06; LR P-value: 3.09E-09; mr1124_2 (Ind_All); LMM P-value: 7.09E-06; mr1149_2 (Ind_All); LR P-value: 2.98E-07; mr1150_2 (All); LMM P-value: 5.96E-06 |
LOC_Os02g39660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g39660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 65.534; most accessible tissue: Callus, score: 79.908 |
| vg0223953318 (J) | chr02 | 23953318 | T | A | 82.40% | 15.21% | T -> A,TCA | NA |
LOC_Os02g39660.1 Alt: A/synonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: A/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g39660.1 Alt: TCA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 65.636; most accessible tissue: Callus, score: 79.908 |
| vg0223953328 (J) | chr02 | 23953328 | A | G | 82.30% | 15.38% | A -> G | NA |
LOC_Os02g39660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 64.269; most accessible tissue: Minghui63 root, score: 77.009 |
| vg0223953379 (J) | chr02 | 23953379 | A | G | 80.60% | 16.17% | A -> G | NA |
LOC_Os02g39660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 60.299; most accessible tissue: Minghui63 panicle, score: 73.225 |
| vg0223953383 (J) | chr02 | 23953383 | T | G | 82.20% | 15.72% | T -> G | NA |
LOC_Os02g39660.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 60.442; most accessible tissue: Minghui63 panicle, score: 73.225 |
| vg0223953389 (J) | chr02 | 23953389 | T | C | 68.10% | 16.61% | T -> C |
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g39660.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 60.072; most accessible tissue: Minghui63 panicle, score: 73.225 |
|
| vg0223953391 (J) | chr02 | 23953391 | T | C | 82.30% | 15.72% | T -> C | NA |
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g39660.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 59.878; most accessible tissue: Minghui63 panicle, score: 73.225 |
| vg0223953398 (J) | chr02 | 23953398 | G | T | 82.40% | 15.87% | G -> T | NA |
LOC_Os02g39660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 59.935; most accessible tissue: Minghui63 panicle, score: 73.225 |
| vg0223953408 (J) | chr02 | 23953408 | C | A | 82.30% | 15.70% | C -> A | NA |
LOC_Os02g39660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 59.597; most accessible tissue: Minghui63 panicle, score: 73.225 |
| vg0223953420 (J) | chr02 | 23953420 | A | C | 82.40% | 15.53% | A -> C | NA |
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g39660.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 58.807; most accessible tissue: Minghui63 panicle, score: 73.225 |
| vg0223953424 (J) | chr02 | 23953424 | C | T | 83.00% | 16.12% | C -> T | NA |
LOC_Os02g39660.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 56.848; most accessible tissue: Minghui63 panicle, score: 70.194 |
| vg0223953426 (J) | chr02 | 23953426 | C | A | 82.60% | 15.87% | C -> A | NA |
LOC_Os02g39660.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 58.678; most accessible tissue: Callus, score: 82.395 |
| vg0223953436 (J) | chr02 | 23953436 | T | A | 82.40% | 15.57% | T -> A | NA |
LOC_Os02g39660.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 58.529; most accessible tissue: Callus, score: 82.395 |
| vg0223953444 (J) | chr02 | 23953444 | C | T | 82.40% | 15.59% | C -> T | NA |
LOC_Os02g39660.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g39660.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 60.026; most accessible tissue: Callus, score: 82.395 |
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