8 variations found. Os04g0386900/LOC_Os04g31730 (expressed protein), ranging from 18,997,865 bp to 18,998,795 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os04g31730 | expressed protein; RAP ID: Os04g0386900; MSU ID: LOC_Os04g31730 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0418997870 (J) | chr04 | 18997870 | A | AGT | 97.40% | 0.00% | A -> AGT | NA |
LOC_Os04g31730.1 Alt: AGT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g31700.1 Alt: AGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31740.1 Alt: AGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31710.1 Alt: AGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31720.1 Alt: AGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.903; most accessible tissue: Callus, score: 74.819 |
| vg0418997871 (J) | chr04 | 18997871 | A | T | 97.40% | 0.00% | A -> T | NA |
LOC_Os04g31730.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g31700.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31720.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.903; most accessible tissue: Callus, score: 74.819 |
| vg0418997883 (J) | chr04 | 18997883 | T | A | 97.40% | 0.00% | T -> A | NA |
LOC_Os04g31730.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g31700.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31740.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31720.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.814; most accessible tissue: Callus, score: 74.819 |
| vg0418998002 (J) | chr04 | 18998002 | G | GGCA | 98.00% | 0.00% | G -> GGCA | NA |
LOC_Os04g31730.1 Alt: GGCA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g31740.1 Alt: GGCA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31710.1 Alt: GGCA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31720.1 Alt: GGCA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.425; most accessible tissue: Callus, score: 85.546 |
| vg0418998438 (J) | chr04 | 18998438 | A | AT | 69.80% | 0.00% | A -> AT,ATT,ATT T,ATTTT | NA |
LOC_Os04g31740.1 Alt: ATTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g31710.1 Alt: ATTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31720.1 Alt: ATTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31730.1 Alt: ATTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31740.1 Alt: ATTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31710.1 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31720.1 Alt: ATTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31730.1 Alt: ATTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31740.1 Alt: ATT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31710.1 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31720.1 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31730.1 Alt: ATT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31740.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31710.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31720.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31730.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.238; most accessible tissue: Minghui63 panicle, score: 92.526 |
| vg0418998442 (J) | chr04 | 18998442 | A | T | 65.30% | 0.00% | A -> T |
LOC_Os04g31740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g31710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31720.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g31730.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.119; most accessible tissue: Minghui63 panicle, score: 92.666 |
|
| vg0418998451 (J) | chr04 | 18998451 | TGG | T | 99.70% | 0.00% | TGG -> T | NA |
LOC_Os04g31730.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os04g31740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os04g31710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g31720.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 80.385; most accessible tissue: Minghui63 panicle, score: 92.928 |
| STR0418998003 (J) | chr04 | 18998003 | GCAG | GCAGCAG | 93.30% | 0.00% | GCAG -> GCAGCAG | NA |
|