204 variations found. Os01g0603800/LOC_Os01g41930 (leucine rich repeat protein; putative; expressed), ranging from 23,775,860 bp to 23,779,747 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g41930 | leucine rich repeat protein, putative, expressed; RAP ID: Os01g0603800; MSU ID: LOC_Os01g41930 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0123775860 (J) | chr01 | 23775860 | GT | GTTTT | 21.60% | 56.14% | GT -> GTTT,GTTTT ,GTTTTT,GT T,G | NA |
LOC_Os01g41930.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g41920.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41930.1 Alt: GTTTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41920.1 Alt: GTTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: GTTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41930.1 Alt: GTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41920.1 Alt: GTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: GTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41930.1 Alt: GTTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41920.1 Alt: GTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: GTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41930.1 Alt: GTTTTT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41920.1 Alt: GTTTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: GTTTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.782; most accessible tissue: Callus, score: 62.341 |
| vg0123775878 (J) | chr01 | 23775878 | C | T | 42.90% | 53.47% | C -> T | NA |
LOC_Os01g41930.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g41920.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.918; most accessible tissue: Callus, score: 62.341 |
| vg0123775879 (J) | chr01 | 23775879 | A | G | 42.90% | 53.15% | A -> G | NA |
LOC_Os01g41930.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g41920.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.918; most accessible tissue: Callus, score: 62.341 |
| vg0123775888 (J) | chr01 | 23775888 | T | C | 44.40% | 54.15% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g41930.1 Alt: C| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os01g41930.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41920.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 10.918; most accessible tissue: Callus, score: 62.341 |
| vg0123775896 (J) | chr01 | 23775896 | C | T | 28.30% | 55.25% | C -> T |
LOC_Os01g41930.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g41920.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.918; most accessible tissue: Callus, score: 62.341 |
|
| vg0123775932 (J) | chr01 | 23775932 | C | CAA | 42.70% | 54.08% | C -> CAA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g41930.1 Alt: CAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41920.1 Alt: CAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 13.979; most accessible tissue: Callus, score: 87.572 |
| vg0123776002 (J) | chr01 | 23776002 | G | A | 24.20% | 55.59% | G -> A | NA |
LOC_Os01g41930.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g41920.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 13.914; most accessible tissue: Callus, score: 87.572 |
| vg0123776036 (J) | chr01 | 23776036 | T | C | 42.90% | 54.27% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g41930.1 Alt: C| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os01g41930.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41920.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 13.914; most accessible tissue: Callus, score: 87.572 |
| vg0123776054 (J) | chr01 | 23776054 | C | T | 42.70% | 54.55% | C -> T | NA |
LOC_Os01g41930.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g41930.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41920.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.107; most accessible tissue: Callus, score: 87.572 |
| vg0123776065 (J) | chr01 | 23776065 | A | G | 32.60% | 55.35% | A -> G |
LOC_Os01g41930.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g41920.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 14.107; most accessible tissue: Callus, score: 87.572 |
|
| vg0123776101 (J) | chr01 | 23776101 | C | CT | 44.30% | 54.70% | C -> CT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g41930.1 Alt: CT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41920.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 12.935; most accessible tissue: Callus, score: 73.338 |
| vg0123776102 (J) | chr01 | 23776102 | A | T | 44.20% | 54.76% | A -> T | NA |
LOC_Os01g41930.1 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g41930.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41920.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 12.935; most accessible tissue: Callus, score: 73.338 |
| vg0123776149 (J) | chr01 | 23776149 | C | T | 43.70% | 53.81% | C -> T | NA |
LOC_Os01g41930.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g41920.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 12.935; most accessible tissue: Callus, score: 73.338 |
| vg0123776332 (J) | chr01 | 23776332 | T | A | 43.20% | 53.22% | T -> A | NA |
LOC_Os01g41930.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g41920.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 41.392; most accessible tissue: Minghui63 root, score: 76.425 |
| vg0123776363 (J) | chr01 | 23776363 | G | T | 32.50% | 55.63% | G -> T |
LOC_Os01g41930.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g41920.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g41910.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 43.525; most accessible tissue: Minghui63 root, score: 77.565 |
|
| vg0123776512 (J) | chr01 | 23776512 | T | C | 25.60% | 56.14% | T -> C |
mr1484 (All); LR P-value: 6.08E-17;
mr1815 (All); LR P-value: 1.65E-06; mr1925 (Jap_All); LR P-value: 2.91E-06; mr1945 (All); LR P-value: 1.21E-11; mr1013_2 (All); LR P-value: 1.88E-15; mr1268_2 (Jap_All); LR P-value: 5.42E-06; mr1808_2 (Jap_All); LR P-value: 1.73E-07; mr1870_2 (Jap_All); LR P-value: 5.67E-06 |
LOC_Os01g41930.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g41930.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 61.698; most accessible tissue: Minghui63 root, score: 85.031 |
| vg0123776530 (J) | chr01 | 23776530 | A | C | 43.60% | 56.22% | A -> C |
LOC_Os01g41930.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g41930.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 66.115; most accessible tissue: Minghui63 root, score: 85.669 |
|
| vg0123776540 (J) | chr01 | 23776540 | G | C | 43.60% | 56.18% | G -> C | NA |
LOC_Os01g41930.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g41930.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 67.920; most accessible tissue: Minghui63 root, score: 86.064 |
| vg0123776551 (J) | chr01 | 23776551 | T | C | 43.50% | 56.26% | T -> C | NA |
LOC_Os01g41930.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g41930.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 69.708; most accessible tissue: Minghui63 root, score: 86.159 |
| vg0123776559 (J) | chr01 | 23776559 | T | G | 43.60% | 56.22% | T -> G | NA |
LOC_Os01g41930.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g41930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 70.068; most accessible tissue: Minghui63 root, score: 86.159 |
| vg0123776566 (J) | chr01 | 23776566 | A | G | 43.60% | 56.20% | A -> G |
LOC_Os01g41930.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g41930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 71.035; most accessible tissue: Minghui63 root, score: 86.253 |
|
| vg0123776580 (J) | chr01 | 23776580 | C | G | 43.60% | 56.20% | C -> G |
LOC_Os01g41930.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g41930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 70.241; most accessible tissue: Minghui63 root, score: 86.438 |
|
| vg0123776584 (J) | chr01 | 23776584 | T | C | 43.60% | 56.12% | T -> C |
LOC_Os01g41930.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g41930.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 70.665; most accessible tissue: Minghui63 root, score: 86.528 |
|
| vg0123776602 (J) | chr01 | 23776602 | C | G | 43.60% | 56.14% | C -> G |
LOC_Os01g41930.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g41930.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 69.832; most accessible tissue: Minghui63 root, score: 85.031 |
|
| vg0123776609 (J) | chr01 | 23776609 | T | C | 43.60% | 18.05% | T -> C |
LOC_Os01g41930.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g41930.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 70.595; most accessible tissue: Minghui63 root, score: 85.252 |
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