67 variations found. Os03g0255500/LOC_Os03g15050 (phosphoenolpyruvate carboxykinase; putative; expressed), ranging from 8,218,790 bp to 8,224,127 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os03g15050 | phosphoenolpyruvate carboxykinase, putative, expressed; RAP ID: Os03g0255500; MSU ID: LOC_Os03g15050 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0308223068 (J) | chr03 | 8223068 | TTT | TT | 85.70% | 0.00% | TTT -> TT | NA |
|
| STR0308223140 (J) | chr03 | 8223140 | TT | TTTTT | 55.20% | 0.00% | TTTT -> TT,TTT,TTT TT | NA |
|
| STR0308224064 (J) | chr03 | 8224064 | GAGGAGG AG | GAGGAG | 88.20% | 0.00% | GAGGAGGAG -> GAGGAG | NA |
|
| vg0308218798 (J) | chr03 | 8218798 | CAAG | C | 96.10% | 0.00% | CAAG -> C | NA |
LOC_Os03g15050.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g15050.4 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15050.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15040.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15040.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.407; most accessible tissue: Callus, score: 93.468 |
| vg0308218818 (J) | chr03 | 8218818 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os03g15050.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g15050.4 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g15050.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g15040.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g15040.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.887; most accessible tissue: Callus, score: 93.468 |
| vg0308218981 (J) | chr03 | 8218981 | C | T | 99.30% | 0.00% | C -> T | NA |
LOC_Os03g15050.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os03g15050.4 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g15050.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os03g15040.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g15040.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.047; most accessible tissue: Callus, score: 97.434 |
| vg0308218985 (J) | chr03 | 8218985 | A | G | 83.50% | 0.00% | G -> A |
LOC_Os03g15050.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g15050.4 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15050.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15040.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15040.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.995; most accessible tissue: Callus, score: 97.434 |
|
| vg0308219015 (J) | chr03 | 8219015 | A | T | 91.30% | 0.17% | A -> T | NA |
LOC_Os03g15050.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g15050.4 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15050.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15040.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15040.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 87.613; most accessible tissue: Callus, score: 97.434 |
| vg0308219228 (J) | chr03 | 8219228 | G | A | 91.70% | 0.00% | G -> A | NA |
LOC_Os03g15050.4 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g15050.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 89.621; most accessible tissue: Callus, score: 97.189 |
| vg0308219404 (J) | chr03 | 8219404 | G | T | 91.70% | 0.00% | G -> T | NA |
LOC_Os03g15050.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
The average chromatin accessibility score: 90.954; most accessible tissue: Zhenshan97 young leaf, score: 97.224 |
| vg0308219465 (J) | chr03 | 8219465 | C | T | 83.40% | 0.00% | T -> C |
LOC_Os03g15050.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g15050.4 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os03g15050.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 90.935; most accessible tissue: Zhenshan97 young leaf, score: 97.355 |
|
| vg0308219850 (J) | chr03 | 8219850 | G | A | 85.00% | 0.00% | G -> A |
mr1779 (All); LR P-value: 4.06E-07;
mr1020_2 (All); LMM P-value: 1.52E-06; LR P-value: 4.32E-10; mr1355_2 (All); LMM P-value: 9.16E-06; LR P-value: 9.19E-09; mr1470_2 (All); LR P-value: 2.17E-06; mr1749_2 (All); LR P-value: 1.30E-08; mr1821_2 (All); LR P-value: 1.79E-09; mr1899_2 (All); LR P-value: 2.47E-06 |
LOC_Os03g15050.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g15050.4 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g15050.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 91.168; most accessible tissue: Zhenshan97 young leaf, score: 96.823 |
| vg0308220015 (J) | chr03 | 8220015 | C | T | 83.30% | 0.00% | T -> C |
LOC_Os03g15050.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g15050.4 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g15050.2 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 92.013; most accessible tissue: Zhenshan97 young leaf, score: 96.414 |
|
| vg0308220060 (J) | chr03 | 8220060 | G | C | 83.10% | 0.02% | G -> C |
LOC_Os03g15050.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g15050.4 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g15050.2 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g15050.4 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g15050.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g15050.2 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 91.273; most accessible tissue: Zhenshan97 young leaf, score: 96.160 |
|
| vg0308220084 (J) | chr03 | 8220084 | G | C | 55.50% | 0.02% | C -> G | NA |
LOC_Os03g15050.4 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g15050.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g15050.2 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g15050.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g15050.4 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g15050.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 90.136; most accessible tissue: Zhenshan97 young leaf, score: 96.311 |
| vg0308220209 (J) | chr03 | 8220209 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os03g15040.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g15040.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15050.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15050.4 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15050.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.754; most accessible tissue: Zhenshan97 young leaf, score: 96.015 |
| vg0308220245 (J) | chr03 | 8220245 | A | G | 68.00% | 0.00% | G -> A | NA |
LOC_Os03g15050.1 Alt: A| splice_region_variant&synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g15050.4 Alt: A| splice_region_variant&synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g15050.2 Alt: A| splice_region_variant&synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 88.876; most accessible tissue: Zhenshan97 young leaf, score: 95.409 |
| vg0308220308 (J) | chr03 | 8220308 | C | T | 96.20% | 0.00% | C -> T | NA |
LOC_Os03g15050.1 Alt: T| splice_region_variant&synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g15050.4 Alt: T| splice_region_variant&synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g15050.2 Alt: T| splice_region_variant&synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 88.716; most accessible tissue: Zhenshan97 young leaf, score: 95.084 |
| vg0308220498 (J) | chr03 | 8220498 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os03g15050.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g15050.4 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os03g15050.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 88.228; most accessible tissue: Zhenshan97 young leaf, score: 93.636 |
| vg0308220647 (J) | chr03 | 8220647 | C | G | 99.80% | 0.00% | C -> G,T | NA |
LOC_Os03g15040.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g15040.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g15050.1 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os03g15050.4 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os03g15050.2 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os03g15040.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g15040.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os03g15050.1 Alt: G| intron_variant MODIFIER(snpEff) LOC_Os03g15050.4 Alt: G| intron_variant MODIFIER(snpEff) LOC_Os03g15050.2 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.552; most accessible tissue: Zhenshan97 root, score: 95.572 |
| vg0308220761 (J) | chr03 | 8220761 | G | A | 83.40% | 0.00% | A -> G |
LOC_Os03g15040.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g15040.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15050.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15050.4 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15050.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.318; most accessible tissue: Zhenshan97 root, score: 95.981 |
|
| vg0308220762 (J) | chr03 | 8220762 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os03g15040.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os03g15040.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15050.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15050.4 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os03g15050.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.174; most accessible tissue: Zhenshan97 root, score: 95.893 |
| vg0308220910 (J) | chr03 | 8220910 | G | A | 84.90% | 0.00% | G -> A |
mr1779 (All); LR P-value: 4.06E-07;
mr1020_2 (All); LMM P-value: 1.52E-06; LR P-value: 4.32E-10; mr1355_2 (All); LMM P-value: 9.16E-06; LR P-value: 9.19E-09; mr1470_2 (All); LR P-value: 2.17E-06; mr1749_2 (All); LR P-value: 1.30E-08; mr1821_2 (All); LR P-value: 1.79E-09; mr1899_2 (All); LR P-value: 2.47E-06 |
LOC_Os03g15050.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os03g15050.4 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) LOC_Os03g15050.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 91.598; most accessible tissue: Zhenshan97 root, score: 96.270 |
| vg0308220988 (J) | chr03 | 8220988 | C | A | 79.20% | 0.06% | C -> A |
LOC_Os03g15050.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g15050.4 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os03g15050.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os03g15050.4 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g15050.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os03g15050.2 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 92.353; most accessible tissue: Zhenshan97 young leaf, score: 95.877 |
|
| vg0308221002 (J) | chr03 | 8221002 | A | G | 98.60% | 0.00% | A -> G | NA |
LOC_Os03g15050.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os03g15050.4 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os03g15050.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 92.674; most accessible tissue: Zhenshan97 young leaf, score: 95.998 |
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