14 variations found. Os03g0336900/LOC_Os03g21870 (DUF623 domain containing protein; expressed), ranging from 12,509,515 bp to 12,510,664 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os03g21870 | DUF623 domain containing protein, expressed; RAP ID: Os03g0336900; MSU ID: LOC_Os03g21870 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0312509713 (J) | chr03 | 12509713 | A | C | 63.00% | 0.00% | C -> A |
LOC_Os03g21870.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 78.644; most accessible tissue: Minghui63 flower, score: 88.549 |
|
| vg0312509752 (J) | chr03 | 12509752 | G | T | 97.40% | 0.00% | G -> T | NA |
LOC_Os03g21870.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 82.137; most accessible tissue: Minghui63 flower, score: 90.931 |
| vg0312509802 (J) | chr03 | 12509802 | A | Unkown | 99.70% | 0.34% | A -> ACGAT | NA |
The average chromatin accessibility score: 84.131; most accessible tissue: Minghui63 flower, score: 91.101
|
| vg0312509810 (J) | chr03 | 12509810 | G | Unkown | 99.70% | 0.34% | G -> A | NA |
LOC_Os03g21870.1 Alt: A| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 84.170; most accessible tissue: Minghui63 flower, score: 91.059 |
| vg0312509812 (J) | chr03 | 12509812 | C | Unkown | 99.70% | 0.34% | C -> T | NA |
LOC_Os03g21870.1 Alt: T| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 84.259; most accessible tissue: Minghui63 flower, score: 91.184 |
| vg0312509824 (J) | chr03 | 12509824 | G | Unkown | 99.70% | 0.21% | G -> A | NA |
LOC_Os03g21870.1 Alt: A| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 84.245; most accessible tissue: Minghui63 flower, score: 91.306 |
| vg0312510030 (J) | chr03 | 12510030 | G | Unkown | 99.80% | 0.13% | G -> C | NA |
LOC_Os03g21870.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g21880.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.836; most accessible tissue: Minghui63 panicle, score: 93.735 |
| vg0312510031 (J) | chr03 | 12510031 | G | Unkown | 99.80% | 0.19% | G -> C | NA |
LOC_Os03g21870.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os03g21880.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.836; most accessible tissue: Minghui63 panicle, score: 93.735 |
| vg0312510083 (J) | chr03 | 12510083 | C | Unkown | 82.50% | 5.33% | C -> T | NA |
LOC_Os03g21870.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g21880.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.991; most accessible tissue: Minghui63 panicle, score: 93.735 |
| vg0312510092 (J) | chr03 | 12510092 | G | Unkown | 82.30% | 5.82% | G -> A | NA |
LOC_Os03g21870.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os03g21880.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.918; most accessible tissue: Minghui63 panicle, score: 93.735 |
| vg0312510163 (J) | chr03 | 12510163 | T | C | 71.70% | 6.58% | T -> C | NA |
LOC_Os03g21870.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os03g21870.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.945; most accessible tissue: Minghui63 panicle, score: 93.735 |
| vg0312510496 (J) | chr03 | 12510496 | G | GCGC | 79.90% | 5.82% | G -> GCGC | NA |
LOC_Os03g21870.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os03g21870.1 Alt: GCGC| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 91.002; most accessible tissue: Zhenshan97 flower, score: 94.869 |
| vg0312510640 (J) | chr03 | 12510640 | GGGA | G | 60.70% | 0.00% | G -> GGGA | NA |
LOC_Os03g21870.1 Alt: GGGA| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 89.701; most accessible tissue: Zhenshan97 flower, score: 95.531 |
| STR0312510641 (J) | chr03 | 12510641 | GGAGGAG GAGGAGG AGGAG | GGAGGAG GAGGAGG AG | 57.20% | 0.00% | GGAGGAGGAG GAGGAG -> GGAGGAGGAG GAGGAGGAG | NA |
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