18 variations found. Os02g0624300/LOC_Os02g41510 (MYB family transcription factor; putative; expressed), ranging from 24,878,774 bp to 24,879,934 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g41510 | MYB family transcription factor, putative, expressed; RAP ID: Os02g0624300; MSU ID: LOC_Os02g41510 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0224878894 (J) | chr02 | 24878894 | A | G | 99.00% | 0.00% | A -> G | NA |
LOC_Os02g41510.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g41500.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.425; most accessible tissue: Minghui63 young leaf, score: 94.199 |
| vg0224878973 (J) | chr02 | 24878973 | G | A | 98.30% | 0.00% | G -> A | NA |
LOC_Os02g41510.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.940; most accessible tissue: Minghui63 young leaf, score: 93.956 |
| vg0224878975 (J) | chr02 | 24878975 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os02g41510.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os02g41500.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 85.921; most accessible tissue: Zhenshan97 root, score: 93.893 |
| vg0224879001 (J) | chr02 | 24879001 | G | A | 99.10% | 0.00% | G -> A | NA |
LOC_Os02g41510.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os02g41500.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.139; most accessible tissue: Zhenshan97 root, score: 94.386 |
| vg0224879221 (J) | chr02 | 24879221 | G | T | 99.90% | 0.00% | G -> T | NA |
LOC_Os02g41510.1 Alt: T| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 88.440; most accessible tissue: Zhenshan97 root, score: 95.161 |
| vg0224879222 (J) | chr02 | 24879222 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os02g41510.1 Alt: A| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 88.701; most accessible tissue: Zhenshan97 root, score: 95.209 |
| vg0224879276 (J) | chr02 | 24879276 | C | T | 98.60% | 0.00% | C -> T | NA |
LOC_Os02g41510.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.909; most accessible tissue: Zhenshan97 young leaf, score: 94.791 |
| vg0224879495 (J) | chr02 | 24879495 | TATCCAA GGCAAAA G | T | 98.70% | 0.00% | TATCCAAGGC AAAAG -> T | NA |
LOC_Os02g41510.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 87.988; most accessible tissue: Zhenshan97 root, score: 96.030 |
| vg0224879522 (J) | chr02 | 24879522 | G | T | 99.50% | 0.00% | G -> T | NA |
LOC_Os02g41510.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 87.871; most accessible tissue: Zhenshan97 root, score: 96.146 |
| vg0224879645 (J) | chr02 | 24879645 | G | T | 99.60% | 0.00% | G -> T | NA |
LOC_Os02g41510.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.271; most accessible tissue: Zhenshan97 root, score: 97.730 |
| vg0224879664 (J) | chr02 | 24879664 | G | A | 87.00% | 0.00% | G -> A |
LOC_Os02g41510.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.560; most accessible tissue: Zhenshan97 root, score: 97.896 |
|
| vg0224879731 (J) | chr02 | 24879731 | G | C | 99.50% | 0.00% | G -> C | NA |
LOC_Os02g41510.1 Alt: C| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 93.591; most accessible tissue: Zhenshan97 root, score: 98.886 |
| vg0224879757 (J) | chr02 | 24879757 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os02g41510.1 Alt: T| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 94.272; most accessible tissue: Zhenshan97 root, score: 99.185 |
| vg0224879763 (J) | chr02 | 24879763 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os02g41510.1 Alt: T| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 94.289; most accessible tissue: Zhenshan97 root, score: 99.190 |
| vg0224879882 (J) | chr02 | 24879882 | G | A | 98.30% | 0.00% | G -> A | NA |
LOC_Os02g41510.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 95.072; most accessible tissue: Zhenshan97 root, score: 99.602 |
| vg0224879887 (J) | chr02 | 24879887 | CTCGGTG TGTGTGT GTGTTGC TGATGCT GCGTCG | C | 86.80% | 0.00% | CTCGGTGTGT GTGTGTGTTG CTGATGCTGC GTCG -> C | NA |
LOC_Os02g41510.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 95.062; most accessible tissue: Zhenshan97 root, score: 99.610 |
| vg0224879890 (J) | chr02 | 24879890 | GGT | G | 79.40% | 11.55% | GGT -> G,GGTGT | NA |
LOC_Os02g41510.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g41510.1 Alt: GGTGT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 95.041; most accessible tissue: Zhenshan97 root, score: 99.602 |
| STR0224878997 (J) | chr02 | 24878997 | CGACG | CGACA | 98.20% | 0.00% | CGACG -> CGACA | NA |
|