20 variations found. Os11g0270000/LOC_Os11g16970 (carnitine racemase like protein; putative; expressed), ranging from 9,410,400 bp to 9,411,512 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os11g16970 | carnitine racemase like protein, putative, expressed; RAP ID: Os11g0270000; MSU ID: LOC_Os11g16970 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1109410443 (J) | chr11 | 9410443 | A | T | 88.10% | 0.95% | A -> T |
mr1059 (Ind_All); LR P-value: 8.83E-08;
mr1143 (Ind_All); LR P-value: 1.71E-09; mr1167 (Ind_All); LR P-value: 9.38E-09; mr1675 (Ind_All); LR P-value: 1.03E-08; mr1726 (Ind_All); LR P-value: 1.44E-07; mr1829 (All); LR P-value: 1.15E-08; mr1829 (Ind_All); LR P-value: 5.30E-12; mr1842 (Ind_All); LR P-value: 6.53E-07; mr1902 (Ind_All); LR P-value: 1.38E-10; mr1969 (Ind_All); LR P-value: 2.03E-09; mr1995 (Ind_All); LR P-value: 9.40E-10; mr1050_2 (Ind_All); LR P-value: 3.42E-06; mr1167_2 (Ind_All); LR P-value: 7.19E-07; mr1829_2 (Ind_All); LR P-value: 2.49E-12; mr1842_2 (Ind_All); LR P-value: 1.15E-07; mr1902_2 (Ind_All); LR P-value: 4.54E-11 |
LOC_Os11g16970.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g16960.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g16950.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 48.515; most accessible tissue: Callus, score: 73.512 |
| vg1109410604 (J) | chr11 | 9410604 | G | A | 91.70% | 0.59% | G -> A |
LOC_Os11g16970.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g16960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g16950.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 59.158; most accessible tissue: Zhenshan97 young leaf, score: 85.001 |
|
| vg1109410629 (J) | chr11 | 9410629 | G | A | 65.90% | 0.99% | G -> A |
LOC_Os11g16970.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g16960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g16950.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 59.605; most accessible tissue: Zhenshan97 young leaf, score: 85.184 |
|
| vg1109410736 (J) | chr11 | 9410736 | A | G | 59.80% | 0.63% | G -> A | NA |
LOC_Os11g16970.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 73.375; most accessible tissue: Zhenshan97 young leaf, score: 89.339 |
| vg1109410741 (J) | chr11 | 9410741 | A | G | 51.80% | 0.63% | G -> A |
LOC_Os11g16970.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 73.514; most accessible tissue: Zhenshan97 young leaf, score: 89.559 |
|
| vg1109410824 (J) | chr11 | 9410824 | C | G | 97.70% | 0.59% | C -> G | NA |
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g16970.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 75.902; most accessible tissue: Zhenshan97 young leaf, score: 90.547 |
| vg1109410881 (J) | chr11 | 9410881 | A | G | 91.70% | 0.57% | A -> G |
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g16970.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 78.104; most accessible tissue: Zhenshan97 young leaf, score: 91.232 |
|
| vg1109410923 (J) | chr11 | 9410923 | G | T | 98.60% | 0.55% | G -> T | NA |
LOC_Os11g16970.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.236; most accessible tissue: Zhenshan97 young leaf, score: 90.363 |
| vg1109410945 (J) | chr11 | 9410945 | C | T | 59.80% | 0.57% | T -> C | NA |
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g16970.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os11g16970.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 80.763; most accessible tissue: Zhenshan97 young leaf, score: 91.466 |
| vg1109410946 (J) | chr11 | 9410946 | G | A | 88.20% | 0.89% | G -> A |
mr1059 (Ind_All); LR P-value: 8.83E-08;
mr1143 (Ind_All); LR P-value: 1.71E-09; mr1167 (Ind_All); LR P-value: 9.38E-09; mr1675 (Ind_All); LR P-value: 1.03E-08; mr1726 (Ind_All); LR P-value: 1.44E-07; mr1829 (All); LR P-value: 1.15E-08; mr1829 (Ind_All); LR P-value: 5.30E-12; mr1842 (Ind_All); LR P-value: 6.53E-07; mr1902 (Ind_All); LR P-value: 1.38E-10; mr1969 (Ind_All); LR P-value: 2.03E-09; mr1995 (Ind_All); LR P-value: 9.40E-10; mr1050_2 (Ind_All); LR P-value: 3.42E-06; mr1167_2 (Ind_All); LR P-value: 7.19E-07; mr1829_2 (Ind_All); LR P-value: 2.49E-12; mr1842_2 (Ind_All); LR P-value: 1.15E-07; mr1902_2 (Ind_All); LR P-value: 4.54E-11 |
LOC_Os11g16970.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 80.742; most accessible tissue: Zhenshan97 young leaf, score: 91.466 |
| vg1109411125 (J) | chr11 | 9411125 | G | A | 99.30% | 0.61% | G -> A | NA |
LOC_Os11g16970.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os11g16960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g16950.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.373; most accessible tissue: Zhenshan97 young leaf, score: 92.168 |
| vg1109411173 (J) | chr11 | 9411173 | G | C | 98.60% | 0.59% | G -> C | NA |
LOC_Os11g16970.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os11g16960.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g16950.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 78.696; most accessible tissue: Zhenshan97 young leaf, score: 92.477 |
| vg1109411218 (J) | chr11 | 9411218 | C | T | 99.20% | 0.61% | C -> T | NA |
LOC_Os11g16970.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 81.884; most accessible tissue: Zhenshan97 young leaf, score: 92.294 |
| vg1109411224 (J) | chr11 | 9411224 | CGAGGAG | CGAGGAG GAG | 96.90% | 0.61% | CGAGGAG -> CGAGGAGGAG ,C | NA |
LOC_Os11g16970.1 Alt: CGAGGAGGAG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os11g16970.1 Alt: C| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 81.894; most accessible tissue: Zhenshan97 young leaf, score: 92.356 |
| vg1109411271 (J) | chr11 | 9411271 | G | A | 97.80% | 0.59% | G -> A | NA |
LOC_Os11g16970.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 81.125; most accessible tissue: Zhenshan97 young leaf, score: 92.535 |
| vg1109411286 (J) | chr11 | 9411286 | G | A | 99.10% | 0.61% | G -> A | NA |
LOC_Os11g16970.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 80.587; most accessible tissue: Zhenshan97 young leaf, score: 92.035 |
| vg1109411351 (J) | chr11 | 9411351 | C | T | 99.20% | 0.61% | C -> T | NA |
LOC_Os11g16970.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 77.290; most accessible tissue: Zhenshan97 young leaf, score: 91.232 |
| vg1109411383 (J) | chr11 | 9411383 | A | G | 59.60% | 0.63% | G -> A | NA |
LOC_Os11g16970.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.096; most accessible tissue: Zhenshan97 young leaf, score: 90.270 |
| vg1109411427 (J) | chr11 | 9411427 | G | T | 59.80% | 0.63% | T -> G | NA |
LOC_Os11g16970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g16970.1 Alt: G| initiator_codon_variant LOW(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 76.567; most accessible tissue: Zhenshan97 young leaf, score: 90.547 |
| vg1109411445 (J) | chr11 | 9411445 | T | A | 88.20% | 0.61% | T -> A,G |
mr1059 (Ind_All); LR P-value: 1.40E-07;
mr1143 (Ind_All); LR P-value: 3.81E-09; mr1167 (Ind_All); LR P-value: 9.96E-09; mr1675 (Ind_All); LR P-value: 1.46E-08; mr1726 (Ind_All); LR P-value: 3.64E-07; mr1829 (All); LR P-value: 9.31E-08; mr1829 (Ind_All); LR P-value: 1.50E-10; mr1902 (Ind_All); LR P-value: 9.85E-10; mr1969 (Ind_All); LR P-value: 2.10E-09; mr1995 (Ind_All); LR P-value: 1.82E-09; mr1829_2 (Ind_All); LR P-value: 1.31E-11; mr1842_2 (Ind_All); LR P-value: 3.93E-07; mr1902_2 (Ind_All); LR P-value: 1.46E-10 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g16970.1 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os11g16970.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g16960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g16970.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g16960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 74.586; most accessible tissue: Zhenshan97 young leaf, score: 89.339 |