32 variations found. Os10g0542800/LOC_Os10g39670 (protein kinase family protein; putative; expressed), ranging from 21,199,762 bp to 21,204,782 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os10g39670 | protein kinase family protein, putative, expressed; RAP ID: Os10g0542800; MSU ID: LOC_Os10g39670 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1021199771 (J) | chr10 | 21199771 | T | C | 58.30% | 0.00% | C -> T | NA |
LOC_Os10g39670.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021199972 (J) | chr10 | 21199972 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os10g39670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021200026 (J) | chr10 | 21200026 | C | T | 93.70% | 0.00% | C -> T | NA |
LOC_Os10g39670.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021200822 (J) | chr10 | 21200822 | G | GA | 99.40% | 0.00% | G -> GA,GAGCACA CGCAATGGTA AAGTAA,GAG CACAC,GAGC ACACGCAATG GTAAAGTAAG GT | NA |
LOC_Os10g39680.1 Alt: GAGCACACGCAATGGTAAAGTAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: GAGCACACGCAATGGTAAAGTAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39680.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39670.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39680.1 Alt: GAGCACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39670.1 Alt: GAGCACAC| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39680.1 Alt: GAGCACACGCAATGGTAAAGTAAGGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39670.1 Alt: GAGCACACGCAATGGTAAAGTAAGGT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021200823 (J) | chr10 | 21200823 | GCCATTC C | G | 99.70% | 0.00% | GCCATTCC -> G,TCCATTCC | NA |
LOC_Os10g39680.1 Alt: TCCATTCC| upstream_gene_variant MODIFIER(snpEff)
LOC_Os10g39670.1 Alt: TCCATTCC| intron_variant MODIFIER(snpEff) LOC_Os10g39680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g39670.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021200832 (J) | chr10 | 21200832 | A | AC | 99.70% | 0.00% | A -> AC | NA |
LOC_Os10g39680.1 Alt: AC| upstream_gene_variant MODIFIER(snpEff)
LOC_Os10g39670.1 Alt: AC| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021200835 (J) | chr10 | 21200835 | C | G | 99.70% | 0.00% | C -> G | NA |
LOC_Os10g39680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os10g39670.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021200842 (J) | chr10 | 21200842 | C | T | 64.80% | 0.19% | T -> C | NA |
LOC_Os10g39680.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021200882 (J) | chr10 | 21200882 | G | A | 64.30% | 0.32% | A -> G | NA |
LOC_Os10g39680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021200901 (J) | chr10 | 21200901 | A | G | 99.80% | 0.00% | A -> G,T | NA |
LOC_Os10g39680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os10g39670.1 Alt: G| intron_variant MODIFIER(snpEff) LOC_Os10g39680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g39670.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021201007 (J) | chr10 | 21201007 | A | G | 58.40% | 0.11% | G -> A | NA |
LOC_Os10g39680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021201023 (J) | chr10 | 21201023 | A | T | 98.90% | 0.00% | A -> T | NA |
LOC_Os10g39680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021201027 (J) | chr10 | 21201027 | G | A | 93.60% | 0.00% | G -> A | NA |
LOC_Os10g39680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021201034 (J) | chr10 | 21201034 | A | G | 58.50% | 0.04% | G -> A | NA |
LOC_Os10g39680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021201072 (J) | chr10 | 21201072 | G | Unkown | 96.70% | 1.27% | G -> A | NA |
LOC_Os10g39680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os10g39670.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021201077 (J) | chr10 | 21201077 | C | T | 65.10% | 0.00% | T -> C | NA |
LOC_Os10g39680.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021201164 (J) | chr10 | 21201164 | G | T | 93.60% | 0.00% | G -> T | NA |
LOC_Os10g39680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021201487 (J) | chr10 | 21201487 | G | A | 93.70% | 0.00% | G -> A | NA |
LOC_Os10g39680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021201778 (J) | chr10 | 21201778 | T | C | 65.10% | 0.00% | C -> T | NA |
LOC_Os10g39680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021201875 (J) | chr10 | 21201875 | C | G | 99.70% | 0.00% | C -> G | NA |
LOC_Os10g39680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os10g39670.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021202066 (J) | chr10 | 21202066 | C | T | 93.70% | 0.00% | C -> T | NA |
LOC_Os10g39680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021202569 (J) | chr10 | 21202569 | T | C | 93.70% | 0.00% | T -> C | NA |
LOC_Os10g39680.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021202776 (J) | chr10 | 21202776 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os10g39680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os10g39670.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021203352 (J) | chr10 | 21203352 | C | T | 93.70% | 0.00% | C -> T | NA |
LOC_Os10g39680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021203353 (J) | chr10 | 21203353 | A | T | 65.10% | 0.00% | T -> A | NA |
LOC_Os10g39680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39670.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021203566 (J) | chr10 | 21203566 | G | C | 99.70% | 0.00% | G -> C | NA |
LOC_Os10g39670.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021203586 (J) | chr10 | 21203586 | C | T | 93.70% | 0.00% | C -> T | NA |
LOC_Os10g39670.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021203857 (J) | chr10 | 21203857 | C | T | 58.60% | 0.00% | T -> C | NA |
LOC_Os10g39670.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021204375 (J) | chr10 | 21204375 | G | A | 64.90% | 0.08% | A -> G | NA |
LOC_Os10g39670.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39690.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021204435 (J) | chr10 | 21204435 | ATTAAAA AGGAAAA CCCAT | A | 93.70% | 0.00% | ATTAAAAAGG AAAACCCAT -> A | NA |
LOC_Os10g39670.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021204565 (J) | chr10 | 21204565 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os10g39670.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os10g39680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os10g39690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1021204648 (J) | chr10 | 21204648 | A | G | 93.70% | 0.00% | A -> G | NA |
LOC_Os10g39670.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os10g39680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os10g39690.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |