284 variations found. Os11g0550100/LOC_Os11g34880 (NB-ARC domain containing protein; expressed), ranging from 20,444,816 bp to 20,450,284 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os11g34880 | NB-ARC domain containing protein, expressed; RAP ID: Os11g0550100; MSU ID: LOC_Os11g34880 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1120444821 (J) | chr11 | 20444821 | TA | T | 70.10% | 20.50% | TA -> T,TAA | NA |
LOC_Os11g34880.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g34880.1 Alt: TAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 39.617; most accessible tissue: Callus, score: 69.352 |
| vg1120444834 (J) | chr11 | 20444834 | C | T | 77.60% | 19.68% | C -> T | NA |
LOC_Os11g34880.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 35.831; most accessible tissue: Minghui63 flower, score: 63.410 |
| vg1120444838 (J) | chr11 | 20444838 | G | T | 77.60% | 19.74% | G -> T | NA |
LOC_Os11g34880.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 35.590; most accessible tissue: Minghui63 flower, score: 62.973 |
| vg1120444867 (J) | chr11 | 20444867 | T | G | 77.30% | 16.50% | T -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g34880.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 34.555; most accessible tissue: Minghui63 flower, score: 60.681 |
| vg1120444882 (J) | chr11 | 20444882 | A | G | 80.20% | 15.28% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g34880.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 34.996; most accessible tissue: Minghui63 flower, score: 62.076 |
| vg1120444886 (J) | chr11 | 20444886 | C | A | 77.20% | 13.01% | C -> A | NA |
LOC_Os11g34880.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 35.141; most accessible tissue: Minghui63 flower, score: 62.529 |
| vg1120444915 (J) | chr11 | 20444915 | G | T | 77.30% | 15.04% | G -> T | NA |
LOC_Os11g34880.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 36.251; most accessible tissue: Minghui63 flower, score: 62.973 |
| vg1120444927 (J) | chr11 | 20444927 | G | A | 81.80% | 15.91% | G -> A | NA |
LOC_Os11g34880.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 38.900; most accessible tissue: Callus, score: 74.376 |
| vg1120444961 (J) | chr11 | 20444961 | G | A | 53.80% | 22.18% | G -> A |
LOC_Os11g34880.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 38.552; most accessible tissue: Callus, score: 74.376 |
|
| vg1120444968 (J) | chr11 | 20444968 | C | T | 77.90% | 20.55% | C -> T | NA |
LOC_Os11g34880.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 38.509; most accessible tissue: Callus, score: 74.376 |
| vg1120444992 (J) | chr11 | 20444992 | G | A | 57.90% | 22.87% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g34880.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 38.250; most accessible tissue: Callus, score: 74.376 |
| vg1120445037 (J) | chr11 | 20445037 | C | T | 57.90% | 23.13% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g34880.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 40.801; most accessible tissue: Callus, score: 74.376 |
| vg1120445038 (J) | chr11 | 20445038 | T | C | 73.40% | 21.48% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g34880.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 40.801; most accessible tissue: Callus, score: 74.376 |
| vg1120445097 (J) | chr11 | 20445097 | A | G | 78.40% | 20.72% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g34880.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 41.439; most accessible tissue: Zhenshan97 young leaf, score: 73.540 |
| vg1120445117 (J) | chr11 | 20445117 | A | G | 78.30% | 20.27% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g34880.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 40.329; most accessible tissue: Zhenshan97 young leaf, score: 72.340 |
| vg1120445123 (J) | chr11 | 20445123 | C | A | 78.30% | 20.82% | C -> A | NA |
LOC_Os11g34880.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 40.033; most accessible tissue: Zhenshan97 young leaf, score: 71.497 |
| vg1120445222 (J) | chr11 | 20445222 | C | T | 57.90% | 17.41% | T -> C | NA |
LOC_Os11g34880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g34880.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 40.394; most accessible tissue: Callus, score: 91.905 |
| vg1120445314 (J) | chr11 | 20445314 | A | T | 78.40% | 19.72% | A -> T | NA |
LOC_Os11g34880.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g34880.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 43.046; most accessible tissue: Callus, score: 91.905 |
| vg1120445376 (J) | chr11 | 20445376 | C | A | 75.00% | 20.38% | C -> A |
LOC_Os11g34880.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g34880.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 42.013; most accessible tissue: Callus, score: 85.408 |
|
| vg1120445396 (J) | chr11 | 20445396 | T | G | 78.30% | 21.20% | T -> G | NA |
LOC_Os11g34880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g34880.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 44.276; most accessible tissue: Callus, score: 85.408 |
| vg1120445414 (J) | chr11 | 20445414 | A | T | 49.10% | 22.68% | T -> A | NA |
LOC_Os11g34880.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g34880.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 43.889; most accessible tissue: Callus, score: 85.408 |
| vg1120445457 (J) | chr11 | 20445457 | A | G | 78.40% | 20.31% | A -> G | NA |
LOC_Os11g34880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g34880.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 43.307; most accessible tissue: Callus, score: 95.124 |
| vg1120445550 (J) | chr11 | 20445550 | T | G | 77.90% | 20.65% | T -> G | NA |
LOC_Os11g34880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g34880.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 44.690; most accessible tissue: Callus, score: 95.124 |
| vg1120445551 (J) | chr11 | 20445551 | A | T | 83.60% | 15.83% | A -> T | NA |
LOC_Os11g34880.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g34880.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 44.743; most accessible tissue: Callus, score: 95.124 |
| vg1120445554 (J) | chr11 | 20445554 | G | C | 77.90% | 20.55% | G -> C | NA |
LOC_Os11g34880.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g34880.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 44.450; most accessible tissue: Callus, score: 95.124 |
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