44 variations found. Os02g0814600/LOC_Os02g56950 (expressed protein), ranging from 34,905,433 bp to 34,910,822 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g56950 | expressed protein; RAP ID: Os02g0814600; MSU ID: LOC_Os02g56950 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0234907295 (J) | chr02 | 34907295 | AAA | AA | 73.30% | 0.00% | AA -> AAA | NA |
|
| STR0234909593 (J) | chr02 | 34909593 | A | G | 99.70% | 0.00% | A -> G | NA |
|
| vg0234905499 (J) | chr02 | 34905499 | TGATTCA | T | 99.80% | 0.00% | TGATTCA -> T | NA |
LOC_Os02g56950.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g56930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56950.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.429; most accessible tissue: Callus, score: 80.624 |
| vg0234905709 (J) | chr02 | 34905709 | C | T | 98.50% | 0.00% | C -> T | NA |
LOC_Os02g56950.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.053; most accessible tissue: Callus, score: 82.559 |
| vg0234905719 (J) | chr02 | 34905719 | TG | T | 99.90% | 0.00% | TG -> T | NA |
LOC_Os02g56950.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g56930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56950.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 47.063; most accessible tissue: Callus, score: 82.559 |
| vg0234905723 (J) | chr02 | 34905723 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os02g56950.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 46.926; most accessible tissue: Callus, score: 82.559 |
| vg0234905757 (J) | chr02 | 34905757 | T | C | 98.50% | 0.00% | T -> C | NA |
LOC_Os02g56950.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56930.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 48.945; most accessible tissue: Callus, score: 82.559 |
| vg0234905791 (J) | chr02 | 34905791 | G | A | 71.60% | 0.00% | A -> G |
Grain_width (All); LR P-value: 3.00E-53;
Grain_width (Jap_All); LR P-value: 1.41E-12; mr1125 (Jap_All); LR P-value: 7.59E-06; mr1188 (All); LMM P-value: 6.48E-06; LR P-value: 7.34E-11; mr1278 (All); LR P-value: 1.08E-06; mr1302 (All); LR P-value: 1.46E-08; mr1376 (All); LR P-value: 4.87E-14; mr1392 (All); LR P-value: 7.63E-07; mr1431 (All); LR P-value: 4.87E-14; mr1471 (Jap_All); LR P-value: 2.03E-07; mr1642 (Jap_All); LR P-value: 6.79E-06; mr1810 (All); LR P-value: 1.98E-07; mr1842 (All); LR P-value: 1.76E-17; mr1924 (All); LR P-value: 4.36E-15; mr1933 (All); LR P-value: 9.97E-17; mr1188_2 (All); LR P-value: 2.99E-12; mr1526_2 (All); LMM P-value: 4.66E-07; LR P-value: 1.34E-60; mr1526_2 (Jap_All); LR P-value: 3.04E-10; mr1679_2 (All); LR P-value: 3.52E-21; mr1771_2 (All); LR P-value: 6.00E-40; mr1842_2 (All); LR P-value: 1.21E-16 |
LOC_Os02g56950.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56930.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 47.647; most accessible tissue: Callus, score: 82.559 |
| vg0234906123 (J) | chr02 | 34906123 | C | CA | 99.30% | 0.00% | C -> CA | NA |
LOC_Os02g56960.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56930.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: CA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 47.261; most accessible tissue: Minghui63 root, score: 65.279 |
| vg0234906196 (J) | chr02 | 34906196 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os02g56960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g56930.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56950.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56950.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 46.268; most accessible tissue: Callus, score: 89.612 |
| vg0234906302 (J) | chr02 | 34906302 | T | G | 61.80% | 0.00% | G -> T |
LOC_Os02g56960.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 46.894; most accessible tissue: Callus, score: 89.612 |
|
| vg0234906338 (J) | chr02 | 34906338 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os02g56960.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g56930.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56950.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56950.2 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 51.475; most accessible tissue: Minghui63 root, score: 81.140 |
| vg0234907035 (J) | chr02 | 34907035 | A | T | 98.50% | 0.00% | A -> T | NA |
LOC_Os02g56960.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56940.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.137; most accessible tissue: Callus, score: 99.476 |
| vg0234907201 (J) | chr02 | 34907201 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os02g56960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g56940.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56950.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56950.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 57.132; most accessible tissue: Callus, score: 99.122 |
| vg0234907210 (J) | chr02 | 34907210 | A | G | 98.10% | 0.00% | A -> G | NA |
LOC_Os02g56960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56940.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 56.531; most accessible tissue: Callus, score: 99.122 |
| vg0234907294 (J) | chr02 | 34907294 | GA | G | 73.50% | 0.00% | G -> GA | NA |
LOC_Os02g56960.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56940.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.934; most accessible tissue: Callus, score: 99.122 |
| vg0234907559 (J) | chr02 | 34907559 | C | A | 71.60% | 0.00% | A -> C |
Grain_width (Jap_All); LR P-value: 1.41E-12;
mr1125 (Jap_All); LR P-value: 7.59E-06; mr1188 (All); LR P-value: 1.44E-10; mr1278 (All); LR P-value: 8.26E-07; mr1302 (All); LR P-value: 1.58E-08; mr1376 (All); LR P-value: 5.52E-14; mr1392 (All); LR P-value: 8.33E-07; mr1431 (All); LR P-value: 5.52E-14; mr1471 (Jap_All); LR P-value: 2.03E-07; mr1642 (Jap_All); LR P-value: 6.79E-06; mr1659 (All); LR P-value: 1.93E-07; mr1810 (All); LR P-value: 1.78E-07; mr1842 (All); LR P-value: 1.82E-16; mr1924 (All); LR P-value: 6.71E-15; mr1933 (All); LR P-value: 9.21E-16; mr1188_2 (All); LR P-value: 8.50E-12; mr1386_2 (All); LR P-value: 2.79E-23; mr1526_2 (All); LMM P-value: 6.68E-07; LR P-value: 6.54E-60; mr1526_2 (Jap_All); LR P-value: 3.04E-10 |
LOC_Os02g56950.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56960.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.896; most accessible tissue: Callus, score: 96.356 |
| vg0234907633 (J) | chr02 | 34907633 | CAGGAAG CAATCTG ATGGGTG T | C | 71.30% | 0.00% | C -> CAGGAAGCAA TCTGATGGGT GT | NA |
LOC_Os02g56950.1 Alt: CAGGAAGCAATCTGATGGGTGT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56960.1 Alt: CAGGAAGCAATCTGATGGGTGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.1 Alt: CAGGAAGCAATCTGATGGGTGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: CAGGAAGCAATCTGATGGGTGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: CAGGAAGCAATCTGATGGGTGT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: CAGGAAGCAATCTGATGGGTGT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 49.693; most accessible tissue: Minghui63 root, score: 77.290 |
| vg0234907635 (J) | chr02 | 34907635 | T | G | 79.10% | 8.93% | T -> G | NA |
LOC_Os02g56950.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 49.503; most accessible tissue: Minghui63 root, score: 77.009 |
| vg0234907636 (J) | chr02 | 34907636 | T | G | 79.10% | 8.93% | T -> G | NA |
LOC_Os02g56950.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 49.420; most accessible tissue: Minghui63 root, score: 77.009 |
| vg0234907637 (J) | chr02 | 34907637 | C | A | 79.10% | 8.93% | C -> A | NA |
LOC_Os02g56950.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 49.391; most accessible tissue: Minghui63 root, score: 77.290 |
| vg0234907959 (J) | chr02 | 34907959 | GA | G | 96.40% | 1.59% | GA -> G,GAA | NA |
LOC_Os02g56960.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56940.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56960.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.1 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 46.467; most accessible tissue: Callus, score: 86.944 |
| vg0234907967 (J) | chr02 | 34907967 | AAT | A | 98.00% | 0.00% | AAT -> A | NA |
LOC_Os02g56960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56940.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 46.214; most accessible tissue: Callus, score: 86.944 |
| vg0234907968 (J) | chr02 | 34907968 | AT | A | 98.50% | 0.00% | AT -> A | NA |
LOC_Os02g56960.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g56940.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56940.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g56950.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 46.214; most accessible tissue: Callus, score: 86.944 |
| vg0234908060 (J) | chr02 | 34908060 | TA | T | 99.90% | 0.00% | TA -> T | NA |
LOC_Os02g56960.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g56940.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56940.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g56950.1 Alt: T| intron_variant MODIFIER(snpEff) LOC_Os02g56950.2 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 47.619; most accessible tissue: Callus, score: 86.944 |
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