11 variations found. Os04g0496700/LOC_Os04g41930 (expressed protein), ranging from 24,844,182 bp to 24,845,054 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os04g41930 | expressed protein; RAP ID: Os04g0496700; MSU ID: LOC_Os04g41930 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0424844193 (J) | chr04 | 24844193 | CCT | CCTCTCT | 91.80% | 0.00% | CCT -> CCTCTCT,CC TCT,CCTCTC TCT,C | NA |
LOC_Os04g41930.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41920.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41910.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41950.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41930.1 Alt: CCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41920.1 Alt: CCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41910.1 Alt: CCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41950.1 Alt: CCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41930.1 Alt: CCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41920.1 Alt: CCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41910.1 Alt: CCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41950.1 Alt: CCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41930.1 Alt: CCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41920.1 Alt: CCTCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41910.1 Alt: CCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41950.1 Alt: CCTCTCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.024; most accessible tissue: Zhenshan97 young leaf, score: 99.800 |
| vg0424844293 (J) | chr04 | 24844293 | A | G | 59.90% | 0.00% | G -> A |
mr1379 (All); LR P-value: 4.46E-10;
mr1509 (All); LR P-value: 1.96E-42; mr1558 (All); LR P-value: 1.33E-46; mr1571 (All); LR P-value: 7.75E-23; mr1580 (All); LR P-value: 8.71E-21; mr1731 (All); LR P-value: 5.94E-25; mr1825 (All); LR P-value: 2.13E-18; mr1940 (All); LR P-value: 5.50E-12; mr1298_2 (All); LR P-value: 1.03E-21; mr1580_2 (All); LR P-value: 3.36E-30; mr1698_2 (All); LR P-value: 2.57E-22; mr1731_2 (All); LR P-value: 3.14E-21; mr1825_2 (All); LR P-value: 5.79E-29; mr1922_2 (All); LR P-value: 5.90E-20; mr1924_2 (All); LR P-value: 2.02E-21; mr1940_2 (All); LR P-value: 1.70E-08 |
LOC_Os04g41930.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41920.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41910.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41950.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.133; most accessible tissue: Zhenshan97 young leaf, score: 99.795 |
| vg0424844343 (J) | chr04 | 24844343 | A | G | 59.90% | 0.00% | G -> A |
mr1379 (All); LR P-value: 1.19E-09;
mr1509 (All); LR P-value: 9.61E-43; mr1558 (All); LR P-value: 3.56E-46; mr1571 (All); LR P-value: 8.02E-24; mr1580 (All); LR P-value: 1.13E-20; mr1825 (All); LR P-value: 6.15E-18; mr1335_2 (All); LR P-value: 8.66E-08; mr1524_2 (All); LR P-value: 6.70E-06; mr1578_2 (All); LR P-value: 6.22E-15; mr1580_2 (All); LR P-value: 2.46E-29; mr1666_2 (All); LR P-value: 8.35E-12 |
LOC_Os04g41930.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g41920.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41910.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41950.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.441; most accessible tissue: Zhenshan97 flag leaf, score: 99.731 |
| vg0424844575 (J) | chr04 | 24844575 | A | G | 60.10% | 0.00% | G -> A |
mr1379 (All); LR P-value: 7.02E-10;
mr1509 (All); LR P-value: 4.58E-41; mr1571 (All); LR P-value: 2.31E-23; mr1580 (All); LR P-value: 1.91E-20; mr1825 (All); LR P-value: 6.37E-18; mr1298_2 (All); LR P-value: 1.49E-20; mr1335_2 (All); LR P-value: 6.07E-08; mr1524_2 (All); LR P-value: 7.05E-06; mr1578_2 (All); LR P-value: 3.43E-15; mr1580_2 (All); LR P-value: 1.89E-29; mr1666_2 (All); LR P-value: 7.88E-12; mr1698_2 (All); LR P-value: 4.00E-21; mr1731_2 (All); LR P-value: 8.66E-20 |
LOC_Os04g41930.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 96.834; most accessible tissue: Zhenshan97 flag leaf, score: 99.308 |
| vg0424844631 (J) | chr04 | 24844631 | C | T | 60.10% | 0.00% | T -> C | NA |
LOC_Os04g41930.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.953; most accessible tissue: Zhenshan97 flag leaf, score: 99.202 |
| vg0424844819 (J) | chr04 | 24844819 | CCCGCGA CG | C | 61.40% | 0.00% | C -> CCCGCGACG, CCCGCGACA | NA |
LOC_Os04g41930.1 Alt: CCCGCGACA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os04g41930.1 Alt: CCCGCGACG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 93.987; most accessible tissue: Zhenshan97 flag leaf, score: 98.936 |
| vg0424844822 (J) | chr04 | 24844822 | GACCGCG C | G | 97.10% | 0.00% | GACCGCGC -> G,GCGACACC GCGC | NA |
LOC_Os04g41930.1 Alt: GCGACACCGCGC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os04g41930.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 93.979; most accessible tissue: Zhenshan97 flag leaf, score: 98.936 |
| vg0424844834 (J) | chr04 | 24844834 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os04g41930.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os04g41920.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g41950.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.944; most accessible tissue: Zhenshan97 flag leaf, score: 98.933 |
| vg0424844837 (J) | chr04 | 24844837 | T | G | 99.60% | 0.00% | T -> G | NA |
LOC_Os04g41930.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os04g41920.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g41950.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.900; most accessible tissue: Zhenshan97 flag leaf, score: 98.917 |
| vg0424844879 (J) | chr04 | 24844879 | T | C | 52.20% | 0.00% | C -> T | NA |
LOC_Os04g41930.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.015; most accessible tissue: Zhenshan97 flag leaf, score: 98.846 |
| vg0424845053 (J) | chr04 | 24845053 | G | C | 60.10% | 0.00% | C -> G | NA |
LOC_Os04g41930.1 Alt: G| splice_region_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os04g41930.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41920.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g41950.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.669; most accessible tissue: Zhenshan97 flag leaf, score: 98.491 |