40 variations found. Os06g0695600/LOC_Os06g48040 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 29,059,686 bp to 29,063,780 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os06g48040 | zinc finger, C3HC4 type domain containing protein, expressed; RAP ID: Os06g0695600; MSU ID: LOC_Os06g48040 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0629059771 (J) | chr06 | 29059771 | G | T | 61.30% | 0.47% | G -> T | NA |
LOC_Os06g48040.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 85.127; most accessible tissue: Minghui63 young leaf, score: 92.335 |
| vg0629059848 (J) | chr06 | 29059848 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os06g48040.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
The average chromatin accessibility score: 81.710; most accessible tissue: Minghui63 young leaf, score: 91.206 |
| vg0629060010 (J) | chr06 | 29060010 | C | T | 61.40% | 0.34% | C -> T | NA |
LOC_Os06g48040.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 82.819; most accessible tissue: Minghui63 young leaf, score: 91.282 |
| vg0629060110 (J) | chr06 | 29060110 | G | A | 76.10% | 0.42% | G -> A |
LOC_Os06g48040.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.844; most accessible tissue: Minghui63 young leaf, score: 87.217 |
|
| vg0629060130 (J) | chr06 | 29060130 | C | A | 61.30% | 0.17% | C -> A | NA |
LOC_Os06g48040.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 76.776; most accessible tissue: Minghui63 young leaf, score: 87.965 |
| vg0629060165 (J) | chr06 | 29060165 | T | C | 75.20% | 0.68% | T -> C |
LOC_Os06g48040.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 79.149; most accessible tissue: Minghui63 young leaf, score: 88.874 |
|
| vg0629060172 (J) | chr06 | 29060172 | C | T | 75.10% | 0.66% | C -> T |
LOC_Os06g48040.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 79.360; most accessible tissue: Minghui63 flower, score: 89.033 |
|
| vg0629060323 (J) | chr06 | 29060323 | A | G | 74.70% | 0.49% | A -> G | NA |
LOC_Os06g48040.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g48040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.519; most accessible tissue: Minghui63 flower, score: 88.293 |
| vg0629060615 (J) | chr06 | 29060615 | C | A | 99.10% | 0.00% | C -> A | NA |
LOC_Os06g48040.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 73.687; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 |
| vg0629060655 (J) | chr06 | 29060655 | C | A | 99.10% | 0.00% | C -> A | NA |
LOC_Os06g48040.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 74.239; most accessible tissue: Zhenshan97 flag leaf, score: 86.987 |
| vg0629060911 (J) | chr06 | 29060911 | G | T | 75.20% | 0.61% | G -> T |
LOC_Os06g48040.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 70.391; most accessible tissue: Minghui63 young leaf, score: 83.666 |
|
| vg0629060923 (J) | chr06 | 29060923 | C | A | 99.80% | 0.00% | C -> A | NA |
LOC_Os06g48040.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 70.118; most accessible tissue: Minghui63 young leaf, score: 83.419 |
| vg0629061095 (J) | chr06 | 29061095 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os06g48040.1 Alt: A| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 64.550; most accessible tissue: Minghui63 young leaf, score: 85.028 |
| vg0629061201 (J) | chr06 | 29061201 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os06g48040.1 Alt: A| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 69.312; most accessible tissue: Minghui63 young leaf, score: 85.633 |
| vg0629061313 (J) | chr06 | 29061313 | AGGCAC | A | 77.80% | 0.38% | AGGCAC -> A | NA |
LOC_Os06g48040.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 70.047; most accessible tissue: Minghui63 young leaf, score: 86.378 |
| vg0629061316 (J) | chr06 | 29061316 | C | T | 98.90% | 0.00% | C -> T | NA |
LOC_Os06g48040.1 Alt: T| intron_variant MODIFIER(snpEff)
The average chromatin accessibility score: 70.105; most accessible tissue: Minghui63 young leaf, score: 86.378 |
| vg0629061318 (J) | chr06 | 29061318 | C | CTATTT | 76.20% | 0.38% | C -> CTATTT | NA |
LOC_Os06g48040.1 Alt: CTATTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 70.235; most accessible tissue: Minghui63 young leaf, score: 86.378 |
| vg0629061370 (J) | chr06 | 29061370 | CG | C | 98.30% | 0.00% | CG -> C | NA |
LOC_Os06g48040.1 Alt: C/frameshift_variant(CooVar)
The average chromatin accessibility score: 71.375; most accessible tissue: Minghui63 young leaf, score: 87.677 |
| vg0629061475 (J) | chr06 | 29061475 | C | T | 99.10% | 0.00% | C -> T | NA |
LOC_Os06g48040.1 Alt: T| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 74.254; most accessible tissue: Minghui63 young leaf, score: 84.596 |
| vg0629061594 (J) | chr06 | 29061594 | G | A | 74.70% | 0.53% | G -> A | NA |
LOC_Os06g48040.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g48040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 75.265; most accessible tissue: Minghui63 young leaf, score: 86.891 |
| vg0629061910 (J) | chr06 | 29061910 | C | T | 63.50% | 0.11% | T -> C |
mr1251 (All); LR P-value: 3.00E-27;
mr1253 (All); LR P-value: 7.07E-18; mr1435 (All); LR P-value: 3.81E-36; mr1638 (All); LR P-value: 8.95E-30; mr1968 (All); LR P-value: 2.32E-16; mr1064_2 (All); LR P-value: 3.45E-57; mr1129_2 (All); LR P-value: 2.14E-36; mr1253_2 (All); LR P-value: 7.30E-22; mr1321_2 (All); LR P-value: 1.09E-06; mr1349_2 (All); LR P-value: 1.66E-10 |
LOC_Os06g48040.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g48040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 73.788; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 |
| vg0629061927 (J) | chr06 | 29061927 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os06g48040.1 Alt: T| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 75.666; most accessible tissue: Minghui63 flower, score: 85.386 |
| vg0629062080 (J) | chr06 | 29062080 | G | T | 75.00% | 0.55% | G -> T | NA |
LOC_Os06g48040.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g48040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 71.900; most accessible tissue: Minghui63 flower, score: 83.608 |
| vg0629062192 (J) | chr06 | 29062192 | A | G | 61.30% | 0.47% | A -> G | NA |
LOC_Os06g48040.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g48040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 73.920; most accessible tissue: Minghui63 flower, score: 82.891 |
| vg0629062265 (J) | chr06 | 29062265 | C | T | 61.30% | 0.49% | C -> T | NA |
LOC_Os06g48040.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g48040.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 71.780; most accessible tissue: Minghui63 flower, score: 83.722 |
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