18 variations found. Os12g0567300/LOC_Os12g37970 (MYB family transcription factor; putative; expressed), ranging from 23,325,525 bp to 23,327,055 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os12g37970 | MYB family transcription factor, putative, expressed; RAP ID: Os12g0567300; MSU ID: LOC_Os12g37970 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1223325558 (J) | chr12 | 23325558 | C | T | 99.70% | 0.00% | C -> A,T | NA |
LOC_Os12g37970.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os12g37970.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g37970.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g37960.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g37960.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g37970.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g37970.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g37970.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g37960.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g37960.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 59.336; most accessible tissue: Callus, score: 87.773 |
| vg1223325733 (J) | chr12 | 23325733 | TG | T | 97.50% | 0.00% | TG -> T | NA |
LOC_Os12g37970.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37970.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.073; most accessible tissue: Callus, score: 88.605 |
| vg1223325757 (J) | chr12 | 23325757 | G | A | 96.60% | 0.00% | G -> A | NA |
LOC_Os12g37970.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37970.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.578; most accessible tissue: Callus, score: 88.605 |
| vg1223325839 (J) | chr12 | 23325839 | A | T | 99.80% | 0.00% | A -> T | NA |
LOC_Os12g37970.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os12g37970.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g37970.3 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g37960.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g37960.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 72.653; most accessible tissue: Minghui63 root, score: 86.438 |
| vg1223326195 (J) | chr12 | 23326195 | A | G | 55.20% | 0.59% | A -> G | NA |
LOC_Os12g37970.2 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37970.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os12g37970.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os12g37970.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os12g37970.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os12g37970.3 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 76.619; most accessible tissue: Zhenshan97 young leaf, score: 83.199 |
| vg1223326452 (J) | chr12 | 23326452 | G | T | 67.10% | 0.57% | G -> T |
mr1069 (All); LR P-value: 2.02E-12;
mr1074 (Ind_All); LR P-value: 1.25E-06; mr1098 (Ind_All); LR P-value: 4.88E-06; mr1148 (Ind_All); LR P-value: 1.80E-07; mr1180 (Ind_All); LR P-value: 2.97E-07; mr1222 (All); LR P-value: 1.80E-08; mr1441 (All); LR P-value: 8.75E-14; mr1542 (Ind_All); LR P-value: 9.01E-06; mr1918 (Ind_All); LR P-value: 8.58E-07; mr1098_2 (Ind_All); LR P-value: 4.10E-07; mr1150_2 (Ind_All); LR P-value: 2.47E-07; mr1222_2 (All); LR P-value: 1.10E-08; mr1227_2 (All); LR P-value: 3.93E-07; mr1607_2 (All); LR P-value: 1.14E-07 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37960.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.3 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.098; most accessible tissue: Zhenshan97 flower, score: 82.718 |
| vg1223326459 (J) | chr12 | 23326459 | T | C | 95.50% | 0.00% | T -> C | NA |
LOC_Os12g37970.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os12g37970.2 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.3 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.787; most accessible tissue: Zhenshan97 flower, score: 82.948 |
| vg1223326650 (J) | chr12 | 23326650 | C | T | 94.40% | 0.00% | C -> T |
mr1074 (Ind_All); LR P-value: 1.91E-06;
mr1081 (Ind_All); LR P-value: 3.47E-06; mr1098 (Ind_All); LR P-value: 1.49E-06; mr1130 (Ind_All); LR P-value: 3.74E-08; mr1148 (Ind_All); LR P-value: 6.36E-07; mr1254 (Ind_All); LR P-value: 7.77E-06; mr1268 (All); LR P-value: 2.39E-06; mr1498 (All); LR P-value: 2.52E-08; mr1769 (All); LR P-value: 1.15E-10; mr1769 (Ind_All); LR P-value: 2.29E-09; mr1918 (Ind_All); LR P-value: 2.66E-06; mr1951 (All); LR P-value: 2.21E-08 |
LOC_Os12g37970.3 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37960.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.539; most accessible tissue: Zhenshan97 flower, score: 85.807 |
| vg1223326796 (J) | chr12 | 23326796 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os12g37970.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.823; most accessible tissue: Zhenshan97 panicle, score: 87.126 |
| vg1223326820 (J) | chr12 | 23326820 | T | A | 92.50% | 0.00% | T -> A | NA |
LOC_Os12g37970.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 80.741; most accessible tissue: Zhenshan97 panicle, score: 86.058 |
| vg1223326821 (J) | chr12 | 23326821 | A | G | 55.00% | 0.61% | A -> G |
LOC_Os12g37970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37970.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 80.741; most accessible tissue: Zhenshan97 panicle, score: 86.058 |
|
| vg1223326846 (J) | chr12 | 23326846 | T | C | 55.00% | 0.61% | T -> C |
LOC_Os12g37970.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37970.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 79.678; most accessible tissue: Zhenshan97 panicle, score: 86.058 |
|
| vg1223326871 (J) | chr12 | 23326871 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os12g37970.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37970.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.802; most accessible tissue: Zhenshan97 young leaf, score: 87.004 |
| vg1223326890 (J) | chr12 | 23326890 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os12g37970.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37970.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.3 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.660; most accessible tissue: Minghui63 root, score: 87.595 |
| vg1223326911 (J) | chr12 | 23326911 | G | A | 99.50% | 0.00% | G -> A,C | NA |
LOC_Os12g37970.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os12g37970.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g37970.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g37960.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g37960.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g37970.1 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff) LOC_Os12g37970.2 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff) LOC_Os12g37970.3 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff) LOC_Os12g37970.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g37970.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g37970.3 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os12g37960.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g37960.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.676; most accessible tissue: Minghui63 root, score: 88.381 |
| vg1223327027 (J) | chr12 | 23327027 | A | G | 94.20% | 2.31% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g37970.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.3 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.950; most accessible tissue: Minghui63 root, score: 89.131 |
| vg1223327036 (J) | chr12 | 23327036 | CACTTTG GTTTGTT | C | 97.50% | 0.00% | CACTTTGGTT TGTT -> C | NA |
LOC_Os12g37970.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g37970.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37960.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g37970.2 Alt: C| non_coding_transcript_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.766; most accessible tissue: Minghui63 root, score: 89.247 |
| STR1223327023 (J) | chr12 | 23327023 | AGAGA | AGAGG | 96.10% | 0.00% | AGAGA -> AGAGG | NA |
|