21 variations found. Os04g0394500/LOC_Os04g32350 (RNA polymerase III RPC4 domain containing protein; expressed), ranging from 19,398,844 bp to 19,401,436 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os04g32350 | RNA polymerase III RPC4 domain containing protein, expressed; RAP ID: Os04g0394500; MSU ID: LOC_Os04g32350 |
Rice quantitative trait nucleotides (QTNs) and inferred QTN effects are from Wei et al., Nature Genetics, 2021.
| Category | Variant ID | Chrom | Pos | Gene | MSU | RAP | Alt_Allele_Function | Ref_geno | Alt_geno |
|---|---|---|---|---|---|---|---|---|---|
| Yield components | vg0419403332 | Chr4 | 19403332 | DGS1/RPC4 | LOC_Os04g32350 | Os04g0394500 | hybrid incompatibility | T | C |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0419398950 (J) | chr04 | 19398950 | G | Unkown | 99.70% | 0.00% | G -> A | NA |
LOC_Os04g32350.1 Alt: A| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 98.920; most accessible tissue: Minghui63 flag leaf, score: 99.965 |
| vg0419399067 (J) | chr04 | 19399067 | C | Unkown | 77.30% | 12.91% | C -> G | NA |
LOC_Os04g32350.1 Alt: G| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 99.014; most accessible tissue: Minghui63 flag leaf, score: 99.970 |
| vg0419399338 (J) | chr04 | 19399338 | G | Unkown | 87.70% | 8.63% | G -> A | NA |
The average chromatin accessibility score: 98.263; most accessible tissue: Minghui63 flag leaf, score: 99.968
|
| vg0419399394 (J) | chr04 | 19399394 | T | A | 99.80% | 0.00% | T -> A | NA |
LOC_Os04g32350.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 98.249; most accessible tissue: Minghui63 flag leaf, score: 99.969 |
| vg0419399468 (J) | chr04 | 19399468 | G | Unkown | 87.80% | 6.96% | G -> T | NA |
LOC_Os04g32350.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 98.758; most accessible tissue: Minghui63 flag leaf, score: 99.958 |
| vg0419399577 (J) | chr04 | 19399577 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os04g32350.1 Alt: A| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 97.916; most accessible tissue: Minghui63 flag leaf, score: 99.968 |
| vg0419399639 (J) | chr04 | 19399639 | C | T | 97.60% | 1.95% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g32350.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.887; most accessible tissue: Minghui63 flag leaf, score: 99.968 |
| vg0419399747 (J) | chr04 | 19399747 | T | Unkown | 46.40% | 51.08% | T -> C | NA |
LOC_Os04g32350.1 Alt: C| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 98.417; most accessible tissue: Minghui63 flag leaf, score: 99.957 |
| vg0419400199 (J) | chr04 | 19400199 | A | Unkown | 41.50% | 53.77% | A -> T | NA |
LOC_Os04g32350.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 97.882; most accessible tissue: Minghui63 flag leaf, score: 99.950 |
| vg0419400230 (J) | chr04 | 19400230 | C | Unkown | 62.70% | 30.24% | C -> T | NA |
LOC_Os04g32350.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 97.804; most accessible tissue: Minghui63 flag leaf, score: 99.941 |
| vg0419400406 (J) | chr04 | 19400406 | C | Unkown | 96.60% | 0.97% | C -> T | NA |
LOC_Os04g32350.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 96.004; most accessible tissue: Minghui63 flag leaf, score: 99.936 |
| vg0419400533 (J) | chr04 | 19400533 | C | Unkown | 54.60% | 42.64% | C -> G | NA |
LOC_Os04g32350.1 Alt: G| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 97.681; most accessible tissue: Minghui63 flag leaf, score: 99.945 |
| vg0419400563 (J) | chr04 | 19400563 | C | Unkown | 53.50% | 43.97% | C -> G,T | NA |
LOC_Os04g32350.1 Alt: G| intron_variant MODIFIER(snpEff)
LOC_Os04g32350.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.622; most accessible tissue: Minghui63 flag leaf, score: 99.938 |
| vg0419400569 (J) | chr04 | 19400569 | GAA | GAAA | 32.70% | 55.82% | GAA -> G,GA,GAAA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g32350.1 Alt: GAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32350.1 Alt: G| intron_variant MODIFIER(snpEff) LOC_Os04g32350.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.602; most accessible tissue: Minghui63 flag leaf, score: 99.936 |
| vg0419400709 (J) | chr04 | 19400709 | T | C | 45.60% | 53.09% | T -> C | NA |
LOC_Os04g32350.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 97.000; most accessible tissue: Minghui63 flag leaf, score: 99.938 |
| vg0419400894 (J) | chr04 | 19400894 | G | Unkown | 88.30% | 10.83% | G -> A | NA |
LOC_Os04g32350.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 94.223; most accessible tissue: Minghui63 flag leaf, score: 99.931 |
| vg0419400928 (J) | chr04 | 19400928 | G | Unkown | 87.30% | 11.93% | G -> A | NA |
LOC_Os04g32350.1 Alt: A| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 96.568; most accessible tissue: Minghui63 flag leaf, score: 99.917 |
| vg0419401156 (J) | chr04 | 19401156 | ACT | ACTCT | 44.20% | 51.27% | ACT -> A,ACTCT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g32350.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g32350.1 Alt: ACTCT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.190; most accessible tissue: Minghui63 flag leaf, score: 99.917 |
| vg0419401336 (J) | chr04 | 19401336 | G | GA | 69.20% | 19.23% | GA -> G,GAA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g32350.1 Alt: GAA| intron_variant MODIFIER(snpEff) LOC_Os04g32350.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.487; most accessible tissue: Minghui63 flag leaf, score: 99.928 |
| vg0419401408 (J) | chr04 | 19401408 | T | Unkown | 99.50% | 0.51% | T -> A | NA |
LOC_Os04g32350.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 94.479; most accessible tissue: Minghui63 flag leaf, score: 99.926 |
| vg0419401413 (J) | chr04 | 19401413 | C | CA | 86.30% | 13.10% | C -> A,CA | NA |
LOC_Os04g32350.1 Alt: CA| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) LOC_Os04g32350.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff) The average chromatin accessibility score: 94.485; most accessible tissue: Minghui63 flag leaf, score: 99.927 |