32 variations found. Os05g0165450/LOC_Os05g07270 (DUF260 domain containing protein; putative; expressed), ranging from 3,843,773 bp to 3,845,480 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os05g07270 | DUF260 domain containing protein, putative; RAP ID: Os05g0165450; MSU ID: LOC_Os05g07270 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0503843879 (J) | chr05 | 3843879 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os05g07270.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.272; most accessible tissue: Zhenshan97 root, score: 86.579 |
| vg0503843921 (J) | chr05 | 3843921 | G | C | 50.70% | 0.00% | C -> G |
LOC_Os05g07270.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 80.861; most accessible tissue: Zhenshan97 root, score: 87.822 |
|
| vg0503843930 (J) | chr05 | 3843930 | TGCG | TGCGGCG GCG | 99.60% | 0.00% | TGCG -> T,TGCGGCGG CG,TGCGGCG | NA |
LOC_Os05g07270.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)
LOC_Os05g07250.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.4 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07270.1 Alt: TGCGGCGGCG| inframe_insertion MODERATE(snpEff) LOC_Os05g07250.1 Alt: TGCGGCGGCG| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.1 Alt: TGCGGCGGCG| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.2 Alt: TGCGGCGGCG| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.4 Alt: TGCGGCGGCG| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.3 Alt: TGCGGCGGCG| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07270.1 Alt: TGCGGCG| inframe_insertion MODERATE(snpEff) LOC_Os05g07250.1 Alt: TGCGGCG| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.1 Alt: TGCGGCG| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.2 Alt: TGCGGCG| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.4 Alt: TGCGGCG| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.3 Alt: TGCGGCG| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.238; most accessible tissue: Zhenshan97 root, score: 87.992 |
| vg0503843986 (J) | chr05 | 3843986 | T | C | 50.60% | 0.00% | C -> T |
LOC_Os05g07270.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 84.298; most accessible tissue: Zhenshan97 root, score: 89.403 |
|
| vg0503844324 (J) | chr05 | 3844324 | T | G | 98.30% | 0.00% | T -> G | NA |
LOC_Os05g07250.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 64.786; most accessible tissue: Callus, score: 84.497 |
| vg0503844345 (J) | chr05 | 3844345 | A | G | 60.60% | 0.19% | G -> A |
mr1644 (All); LR P-value: 7.29E-09;
mr1191_2 (All); LR P-value: 1.23E-14; mr1238_2 (Ind_All); LMM P-value: 2.83E-07; LR P-value: 6.41E-08; mr1484_2 (Ind_All); LMM P-value: 1.70E-06; LR P-value: 9.10E-07; mr1841_2 (Ind_All); LMM P-value: 6.61E-07; LR P-value: 4.59E-08; mr1900_2 (All); LR P-value: 5.16E-21; mr1900_2 (Ind_All); LR P-value: 4.26E-06 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g07260.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.768; most accessible tissue: Zhenshan97 root, score: 72.671 |
| vg0503844349 (J) | chr05 | 3844349 | G | C | 99.70% | 0.00% | G -> C | NA |
LOC_Os05g07260.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.367; most accessible tissue: Zhenshan97 root, score: 72.188 |
| vg0503844364 (J) | chr05 | 3844364 | GT | G | 84.90% | 0.00% | GT -> GTTT,G,GTT ,GTTTT | NA |
LOC_Os05g07260.1 Alt: GTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: GTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: GTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: GTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: GTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.1 Alt: GTTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: GTTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: GTTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: GTTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: GTTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.1 Alt: GTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: GTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: GTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: GTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: GTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.657; most accessible tissue: Zhenshan97 root, score: 69.506 |
| vg0503844372 (J) | chr05 | 3844372 | T | TTA | 58.20% | 6.92% | T -> TTA,TTAA,T TTAA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g07260.1 Alt: TTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: TTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: TTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: TTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: TTA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.1 Alt: TTTAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: TTTAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: TTTAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: TTTAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: TTTAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.1 Alt: TTAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: TTAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: TTAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: TTAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: TTAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.244; most accessible tissue: Callus, score: 68.266 |
| vg0503844373 (J) | chr05 | 3844373 | TA | AA | 67.10% | 11.07% | TA -> AA,T | NA |
LOC_Os05g07260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os05g07260.1 Alt: AA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: AA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: AA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: AA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: AA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 55.371; most accessible tissue: Callus, score: 68.266 |
| vg0503844374 (J) | chr05 | 3844374 | AAT | A | 50.50% | 0.04% | A -> AAT,AT,T | NA |
LOC_Os05g07260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os05g07260.1 Alt: AAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: AAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: AAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: AAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: AAT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.383; most accessible tissue: Callus, score: 68.266 |
| vg0503844375 (J) | chr05 | 3844375 | A | T | 48.30% | 49.32% | A -> T | NA |
LOC_Os05g07260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 54.383; most accessible tissue: Callus, score: 68.266 |
| vg0503844393 (J) | chr05 | 3844393 | A | G | 90.80% | 0.00% | A -> G |
mr1248 (All); LR P-value: 1.77E-08;
mr1248 (Jap_All); LR P-value: 3.69E-09; mr1301 (All); LR P-value: 1.13E-23; mr1410 (All); LR P-value: 9.59E-15; mr1422 (Jap_All); LR P-value: 2.45E-06; mr1510 (All); LR P-value: 2.72E-06; mr1551 (Jap_All); LR P-value: 5.08E-07; mr1554 (All); LR P-value: 7.21E-07; mr1563 (Jap_All); LR P-value: 1.05E-08; mr1593 (All); LR P-value: 1.92E-08; mr1593 (Jap_All); LR P-value: 1.14E-15; mr1648 (All); LR P-value: 2.35E-08; mr1699 (All); LR P-value: 1.46E-31; mr1250_2 (Jap_All); LR P-value: 1.69E-07; mr1301_2 (All); LR P-value: 8.31E-24; mr1354_2 (All); LR P-value: 1.39E-09; mr1410_2 (All); LR P-value: 6.98E-15; mr1563_2 (Jap_All); LR P-value: 1.78E-07; mr1593_2 (All); LR P-value: 1.68E-11; mr1696_2 (All); LR P-value: 9.77E-08; mr1699_2 (All); LR P-value: 6.84E-31; mr1705_2 (All); LR P-value: 1.56E-11; mr1705_2 (Jap_All); LR P-value: 1.07E-07; mr1733_2 (Jap_All); LR P-value: 1.33E-07; mr1993_2 (All); LR P-value: 6.28E-12 |
LOC_Os05g07260.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 52.477; most accessible tissue: Callus, score: 68.266 |
| vg0503844471 (J) | chr05 | 3844471 | A | C | 91.60% | 0.00% | A -> C | NA |
LOC_Os05g07260.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 45.857; most accessible tissue: Callus, score: 80.816 |
| vg0503844477 (J) | chr05 | 3844477 | GATAT | GATATAT | 92.30% | 0.00% | GATAT -> GATATAT,GA TATATAT,GA TATATATATA TAT,G | NA |
LOC_Os05g07260.1 Alt: GATATATAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: GATATATAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: GATATATAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: GATATATAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: GATATATAT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.4 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07270.1 Alt: G| intron_variant MODIFIER(snpEff) LOC_Os05g07260.1 Alt: GATATAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: GATATAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: GATATAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: GATATAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: GATATAT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.1 Alt: GATATATATATATAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: GATATATATATATAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: GATATATATATATAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: GATATATATATATAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: GATATATATATATAT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 44.501; most accessible tissue: Callus, score: 80.816 |
| vg0503844500 (J) | chr05 | 3844500 | A | G | 94.40% | 0.00% | A -> G | NA |
LOC_Os05g07260.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 43.023; most accessible tissue: Callus, score: 80.816 |
| vg0503844538 (J) | chr05 | 3844538 | TTTC | T | 99.70% | 0.00% | TTTC -> T | NA |
LOC_Os05g07260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 38.065; most accessible tissue: Callus, score: 80.816 |
| vg0503844573 (J) | chr05 | 3844573 | T | C | 91.50% | 0.00% | T -> C | NA |
LOC_Os05g07260.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 33.991; most accessible tissue: Callus, score: 80.816 |
| vg0503844587 (J) | chr05 | 3844587 | A | AT | 91.50% | 0.00% | A -> AT,ATT | NA |
LOC_Os05g07260.1 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: ATT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 31.923; most accessible tissue: Callus, score: 45.271 |
| vg0503844669 (J) | chr05 | 3844669 | T | TAA | 92.50% | 0.00% | T -> TAA,TA,TAA A | NA |
LOC_Os05g07260.1 Alt: TAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: TAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: TAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: TAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: TAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.1 Alt: TAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.2 Alt: TAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: TAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: TAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: TAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 27.804; most accessible tissue: Callus, score: 45.271 |
| vg0503844677 (J) | chr05 | 3844677 | G | T | 92.60% | 0.00% | G -> T | NA |
LOC_Os05g07260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 32.135; most accessible tissue: Callus, score: 65.885 |
| vg0503844727 (J) | chr05 | 3844727 | A | T | 99.40% | 0.00% | A -> T | NA |
LOC_Os05g07260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 31.976; most accessible tissue: Callus, score: 65.885 |
| vg0503844749 (J) | chr05 | 3844749 | G | C | 92.50% | 0.00% | G -> C |
mr1113 (All); LR P-value: 9.89E-16;
mr1117 (All); LR P-value: 9.43E-20; mr1119 (All); LR P-value: 6.84E-17; mr1120 (All); LR P-value: 1.19E-22; mr1126 (All); LR P-value: 7.25E-07; mr1231 (All); LR P-value: 1.42E-13; mr1247 (All); LR P-value: 1.46E-21; mr1415 (All); LR P-value: 2.27E-07; mr1522 (All); LR P-value: 5.98E-13; mr1567 (All); LR P-value: 2.27E-07; mr1652 (All); LR P-value: 4.27E-07; mr1665 (All); LR P-value: 5.27E-06; mr1868 (All); LR P-value: 1.53E-24; mr1961 (All); LR P-value: 9.38E-22; mr1113_2 (All); LR P-value: 7.94E-18; mr1117_2 (All); LR P-value: 1.15E-18; mr1119_2 (All); LR P-value: 3.31E-18; mr1120_2 (All); LR P-value: 1.67E-23; mr1247_2 (All); LR P-value: 7.02E-23; mr1305_2 (All); LR P-value: 2.16E-20; mr1522_2 (All); LR P-value: 1.13E-06; mr1911_2 (All); LR P-value: 1.83E-14; mr1929_2 (All); LR P-value: 2.24E-06; mr1961_2 (All); LR P-value: 1.16E-18 |
LOC_Os05g07260.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 32.061; most accessible tissue: Callus, score: 65.885 |
| vg0503844768 (J) | chr05 | 3844768 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os05g07260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 31.676; most accessible tissue: Callus, score: 65.885 |
| vg0503844785 (J) | chr05 | 3844785 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os05g07260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 31.845; most accessible tissue: Callus, score: 65.885 |
| vg0503844806 (J) | chr05 | 3844806 | T | C | 92.60% | 0.00% | T -> C | NA |
LOC_Os05g07260.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 32.402; most accessible tissue: Callus, score: 65.885 |
| vg0503844815 (J) | chr05 | 3844815 | C | T | 99.30% | 0.00% | C -> T | NA |
LOC_Os05g07260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 32.356; most accessible tissue: Callus, score: 65.885 |
| vg0503844835 (J) | chr05 | 3844835 | G | T | 98.80% | 0.00% | G -> T | NA |
LOC_Os05g07260.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 29.362; most accessible tissue: Minghui63 panicle, score: 50.413 |
| vg0503844889 (J) | chr05 | 3844889 | T | TTTGAG | 91.20% | 0.00% | T -> TTTGAG | NA |
LOC_Os05g07260.1 Alt: TTTGAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g07260.2 Alt: TTTGAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.4 Alt: TTTGAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07260.3 Alt: TTTGAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g07270.1 Alt: TTTGAG| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 34.033; most accessible tissue: Minghui63 panicle, score: 56.842 |
| vg0503845107 (J) | chr05 | 3845107 | A | C | 99.60% | 0.00% | A -> C | NA |
LOC_Os05g07260.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os05g07260.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.4 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07270.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 51.319; most accessible tissue: Minghui63 panicle, score: 68.460 |
| vg0503845180 (J) | chr05 | 3845180 | A | C | 99.90% | 0.00% | A -> C | NA |
LOC_Os05g07260.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os05g07260.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.4 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07260.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g07270.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 59.296; most accessible tissue: Callus, score: 78.056 |
| STR0503844802 (J) | chr05 | 3844802 | TTTTT | TTTTC | 93.90% | 0.00% | TTTTT -> TTTTC | NA |
|