24 variations found. Os01g0159200/LOC_Os01g06580 (fasciclin domain containing protein; expressed), ranging from 3,097,345 bp to 3,098,527 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g06580 | fasciclin domain containing protein, expressed; RAP ID: Os01g0159200; MSU ID: LOC_Os01g06580 |
| MSU ID | RAP ID | Symbol | Name | Explanation | Recommended Gene Symbol | Recommended Gene Name |
|---|---|---|---|---|---|---|
| LOC_Os01g06580 | Os01g0159200 | OsFLA8 | fasciclin-like AGP 8, fasciclin-like arabinogalactan protein 8 | FLA8 | FASCICLIN-LIKE ARABINOGALACTAN PROTEIN 8 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0103097387 (J) | chr01 | 3097387 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os01g06580.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g06560.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g06560.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g06570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.535; most accessible tissue: Zhenshan97 flag leaf, score: 94.594 |
| vg0103097495 (J) | chr01 | 3097495 | CAACAAA AAAAATT AAGAGAG AAAAAAA ACAACA | C | 91.40% | 2.77% | CAACAAAAAA AATTAAGAGA GAAAAAAAAC AACA -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g06580.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.747; most accessible tissue: Zhenshan97 flag leaf, score: 96.657 |
| vg0103097498 (J) | chr01 | 3097498 | C | CA | 88.10% | 0.00% | C -> CA | NA |
LOC_Os01g06580.1 Alt: CA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g06560.1 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: CA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.647; most accessible tissue: Zhenshan97 flag leaf, score: 96.666 |
| vg0103097501 (J) | chr01 | 3097501 | A | C | 99.10% | 0.02% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g06580.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.628; most accessible tissue: Zhenshan97 flag leaf, score: 96.710 |
| vg0103097503 (J) | chr01 | 3097503 | A | G | 83.80% | 0.61% | A -> G |
LOC_Os01g06580.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g06560.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 85.669; most accessible tissue: Zhenshan97 flag leaf, score: 96.735 |
|
| vg0103097507 (J) | chr01 | 3097507 | T | A | 86.50% | 0.76% | T -> A | NA |
LOC_Os01g06580.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g06560.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 85.586; most accessible tissue: Zhenshan97 flag leaf, score: 96.674 |
| vg0103097509 (J) | chr01 | 3097509 | AAG | A | 85.10% | 0.06% | A -> AAG | NA |
LOC_Os01g06580.1 Alt: AAG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g06560.1 Alt: AAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: AAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: AAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: AAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: AAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: AAG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 85.903; most accessible tissue: Zhenshan97 flag leaf, score: 96.752 |
| vg0103097515 (J) | chr01 | 3097515 | G | GAGA | 88.10% | 0.00% | G -> GAGA,GAGAA | NA |
LOC_Os01g06580.1 Alt: GAGAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g06560.1 Alt: GAGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: GAGAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: GAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: GAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: GAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: GAGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06580.1 Alt: GAGA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.1 Alt: GAGA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: GAGA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: GAGA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: GAGA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: GAGA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: GAGA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.010; most accessible tissue: Zhenshan97 flag leaf, score: 96.793 |
| vg0103097517 (J) | chr01 | 3097517 | A | G | 92.30% | 2.60% | A -> G | NA |
LOC_Os01g06580.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g06560.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 85.995; most accessible tissue: Zhenshan97 flag leaf, score: 96.785 |
| vg0103097529 (J) | chr01 | 3097529 | GA | GAA | 88.10% | 0.00% | GA -> GAA,G | NA |
LOC_Os01g06580.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g06560.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06580.1 Alt: GAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.098; most accessible tissue: Zhenshan97 flag leaf, score: 96.826 |
| vg0103097543 (J) | chr01 | 3097543 | A | T | 88.10% | 0.00% | A -> T |
mr1097 (All); LR P-value: 4.90E-11;
mr1097 (Jap_All); LR P-value: 8.79E-06; mr1425 (All); LR P-value: 6.84E-06; mr1671 (Jap_All); LR P-value: 2.16E-07; mr1699 (All); LR P-value: 5.55E-29; mr1097_2 (All); LR P-value: 6.99E-13; mr1363_2 (All); LR P-value: 1.41E-06; mr1369_2 (All); LR P-value: 1.36E-06; mr1453_2 (All); LR P-value: 2.91E-07; mr1699_2 (All); LR P-value: 3.13E-29; mr1769_2 (All); LR P-value: 3.17E-10 |
LOC_Os01g06580.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g06560.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.846; most accessible tissue: Zhenshan97 flag leaf, score: 96.777 |
| vg0103097560 (J) | chr01 | 3097560 | A | G | 84.80% | 0.00% | A -> G |
LOC_Os01g06580.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g06560.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.899; most accessible tissue: Zhenshan97 flag leaf, score: 96.793 |
|
| vg0103097570 (J) | chr01 | 3097570 | C | CG | 88.00% | 0.00% | C -> CG | NA |
LOC_Os01g06580.1 Alt: CG| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g06560.1 Alt: CG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06560.2 Alt: CG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: CG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: CG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: CG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: CG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.521; most accessible tissue: Zhenshan97 flag leaf, score: 96.856 |
| vg0103097639 (J) | chr01 | 3097639 | C | G | 99.60% | 0.00% | C -> G | NA |
LOC_Os01g06580.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os01g06560.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g06560.2 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g06570.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.771; most accessible tissue: Zhenshan97 flag leaf, score: 97.408 |
| vg0103097681 (J) | chr01 | 3097681 | G | A | 87.90% | 0.00% | G -> A |
mr1097 (All); LR P-value: 4.90E-11;
mr1097 (Jap_All); LR P-value: 8.79E-06; mr1425 (All); LR P-value: 6.84E-06; mr1671 (Jap_All); LR P-value: 2.16E-07; mr1699 (All); LR P-value: 5.55E-29; mr1097_2 (All); LR P-value: 6.99E-13; mr1363_2 (All); LR P-value: 1.41E-06; mr1369_2 (All); LR P-value: 1.36E-06; mr1453_2 (All); LR P-value: 2.91E-07; mr1699_2 (All); LR P-value: 3.13E-29; mr1769_2 (All); LR P-value: 3.17E-10 |
LOC_Os01g06580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 90.376; most accessible tissue: Zhenshan97 flag leaf, score: 97.673 |
| vg0103097796 (J) | chr01 | 3097796 | C | T | 97.60% | 0.00% | T -> C | NA |
LOC_Os01g06580.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 92.231; most accessible tissue: Zhenshan97 flag leaf, score: 98.351 |
| vg0103098121 (J) | chr01 | 3098121 | C | T | 84.90% | 0.00% | C -> T |
LOC_Os01g06580.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.076; most accessible tissue: Zhenshan97 flag leaf, score: 98.575 |
|
| vg0103098208 (J) | chr01 | 3098208 | A | G | 60.60% | 0.00% | G -> A |
LOC_Os01g06580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 94.743; most accessible tissue: Zhenshan97 flag leaf, score: 98.732 |
|
| vg0103098229 (J) | chr01 | 3098229 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os01g06580.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os01g06570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.368; most accessible tissue: Zhenshan97 flag leaf, score: 98.606 |
| vg0103098274 (J) | chr01 | 3098274 | C | T | 70.90% | 0.00% | C -> T | NA |
LOC_Os01g06580.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 93.838; most accessible tissue: Zhenshan97 flag leaf, score: 98.396 |
| vg0103098327 (J) | chr01 | 3098327 | C | A | 83.50% | 0.61% | C -> A | NA |
LOC_Os01g06580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g06580.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 93.019; most accessible tissue: Zhenshan97 flag leaf, score: 98.390 |
| vg0103098423 (J) | chr01 | 3098423 | CAAAA | CAA | 28.50% | 7.17% | C -> CAAAA,CAAA ,CAAAAA,CA AAAAA,CAA, CA | NA |
LOC_Os01g06580.1 Alt: CA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g06570.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: CA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06580.1 Alt: CAAAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: CAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06580.1 Alt: CAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: CAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06580.1 Alt: CAAAAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: CAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: CAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: CAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: CAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06580.1 Alt: CAAAAAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: CAAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: CAAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: CAAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: CAAAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g06580.1 Alt: CAAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06570.1 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.1 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.2 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g06590.3 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.886; most accessible tissue: Zhenshan97 flag leaf, score: 98.326 |
| vg0103098429 (J) | chr01 | 3098429 | A | AAAAAT | 99.60% | 0.00% | A -> AAAAAT | NA |
LOC_Os01g06580.1 Alt: AAAAAT| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g06570.1 Alt: AAAAAT| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.1 Alt: AAAAAT| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.2 Alt: AAAAAT| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.3 Alt: AAAAAT| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.777; most accessible tissue: Minghui63 young leaf, score: 98.369 |
| vg0103098491 (J) | chr01 | 3098491 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os01g06580.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g06570.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g06590.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.754; most accessible tissue: Minghui63 young leaf, score: 98.418 |