48 variations found. Os01g0871500/LOC_Os01g65100 (peptide transporter; putative; expressed), ranging from 37,790,110 bp to 37,792,998 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g65100 | peptide transporter, putative, expressed; RAP ID: Os01g0871500; MSU ID: LOC_Os01g65100 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0137791380 (J) | chr01 | 37791380 | GCTGCC | GCTGCT | 47.00% | 0.00% | GCTGCT -> GCTGCC | NA |
|
| STR0137792984 (J) | chr01 | 37792984 | TT | TTT | 98.30% | 0.00% | TT -> TTT | NA |
|
| vg0137790152 (J) | chr01 | 37790152 | CCT | C | 50.70% | 5.92% | C -> CCT,CATCT, CCTCT,CCTC TCTCT,CCTC TCT | NA |
LOC_Os01g65100.3 Alt: CATCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65094.1 Alt: CATCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: CATCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: CATCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: CCTCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65094.1 Alt: CCTCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: CCTCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: CCTCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: CCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65094.1 Alt: CCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: CCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: CCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: CCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65094.1 Alt: CCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: CCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: CCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: CCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65094.1 Alt: CCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: CCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: CCTCTCT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.671; most accessible tissue: Zhenshan97 flower, score: 99.808 |
| vg0137790189 (J) | chr01 | 37790189 | T | C | 58.80% | 5.35% | C -> T | NA |
LOC_Os01g65100.3 Alt: T| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g65100.3 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65094.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 98.972; most accessible tissue: Zhenshan97 flower, score: 99.771 |
| vg0137790345 (J) | chr01 | 37790345 | G | GAA | 88.60% | 2.22% | G -> GAA,GA | NA |
LOC_Os01g65100.1 Alt: GA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65100.3 Alt: GA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65094.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: GAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: GAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65094.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 98.175; most accessible tissue: Zhenshan97 flower, score: 99.713 |
| vg0137790450 (J) | chr01 | 37790450 | T | A | 98.40% | 0.00% | T -> A | NA |
LOC_Os01g65100.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65100.3 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.841; most accessible tissue: Zhenshan97 flower, score: 99.549 |
| vg0137790475 (J) | chr01 | 37790475 | T | C | 64.70% | 0.00% | C -> T | NA |
LOC_Os01g65100.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65100.3 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.577; most accessible tissue: Zhenshan97 flower, score: 99.431 |
| vg0137790714 (J) | chr01 | 37790714 | A | AT | 98.30% | 0.00% | A -> AT | NA |
LOC_Os01g65110.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65100.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.080; most accessible tissue: Zhenshan97 flower, score: 97.789 |
| vg0137790749 (J) | chr01 | 37790749 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os01g65100.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g65100.2 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 90.820; most accessible tissue: Zhenshan97 flower, score: 98.035 |
| vg0137790939 (J) | chr01 | 37790939 | C | T | 77.00% | 0.00% | C -> T |
mr1375 (Ind_All); LR P-value: 9.21E-07;
mr1517 (All); LMM P-value: 8.77E-08; mr1517 (Ind_All); LMM P-value: 3.50E-13; LR P-value: 1.15E-15; mr1538 (All); LMM P-value: 1.90E-07; mr1538 (Ind_All); LMM P-value: 7.18E-11; LR P-value: 1.81E-13; mr1274_2 (All); LR P-value: 7.82E-06; mr1517_2 (All); LMM P-value: 2.19E-08; mr1517_2 (Ind_All); LMM P-value: 4.30E-15; LR P-value: 2.40E-16; mr1538_2 (All); LMM P-value: 5.36E-07; mr1538_2 (Ind_All); LMM P-value: 2.47E-11; LR P-value: 4.24E-17 |
LOC_Os01g65100.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g65100.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 90.238; most accessible tissue: Zhenshan97 flower, score: 98.416 |
| vg0137791079 (J) | chr01 | 37791079 | GA | G | 46.10% | 0.17% | G -> GA,GAA,GAA A,GAAAA | NA |
LOC_Os01g65100.3 Alt: GA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65110.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: GA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: GAAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65110.1 Alt: GAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: GAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: GAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: GAAAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65110.1 Alt: GAAAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: GAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: GAAAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: GAA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65110.1 Alt: GAA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: GAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.904; most accessible tissue: Zhenshan97 flower, score: 97.802 |
| vg0137791280 (J) | chr01 | 37791280 | G | C | 58.90% | 0.00% | C -> G,A |
mr1003 (All); LR P-value: 3.39E-21;
mr1051 (All); LR P-value: 2.88E-21; mr1125 (All); LR P-value: 3.68E-48; mr1179 (All); LR P-value: 6.30E-19; mr1362 (All); LR P-value: 1.11E-12; mr1517 (All); LMM P-value: 8.11E-08; LR P-value: 7.06E-88; mr1538 (All); LMM P-value: 2.00E-06; LR P-value: 4.18E-78; mr1541 (All); LR P-value: 2.08E-20; mr1592 (All); LR P-value: 1.88E-15; mr1657 (All); LR P-value: 9.65E-12; mr1737 (All); LR P-value: 2.92E-33; mr1793 (All); LR P-value: 1.65E-30; mr1051_2 (All); LR P-value: 1.24E-25; mr1151_2 (All); LR P-value: 2.35E-12; mr1458_2 (All); LR P-value: 2.00E-46; mr1509_2 (All); LR P-value: 1.26E-44; mr1517_2 (All); LMM P-value: 1.59E-10; mr1538_2 (All); LMM P-value: 1.24E-07; mr1558_2 (All); LR P-value: 6.80E-57; mr1571_2 (All); LR P-value: 6.38E-32; mr1793_2 (All); LR P-value: 3.97E-46; mr1885_2 (All); LR P-value: 2.09E-07; mr1922_2 (All); LR P-value: 3.15E-19 |
LOC_Os01g65100.3 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65110.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os01g65110.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g65100.1 Alt: A| intron_variant MODIFIER(snpEff) LOC_Os01g65100.2 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.480; most accessible tissue: Zhenshan97 flower, score: 95.519 |
| vg0137791282 (J) | chr01 | 37791282 | C | T | 82.50% | 0.04% | C -> T |
mr1375 (Ind_All); LR P-value: 4.18E-07;
mr1517 (All); LMM P-value: 5.05E-09; mr1517 (Ind_All); LMM P-value: 5.39E-13; LR P-value: 1.42E-15; mr1538 (All); LMM P-value: 4.02E-08; mr1538 (Ind_All); LMM P-value: 1.55E-10; LR P-value: 5.26E-13; mr1517_2 (All); LMM P-value: 9.47E-10; mr1517_2 (Ind_All); LMM P-value: 4.13E-16; LR P-value: 4.70E-17; mr1538_2 (All); LMM P-value: 1.07E-07; mr1538_2 (Ind_All); LMM P-value: 1.96E-11; LR P-value: 3.29E-17 |
LOC_Os01g65100.3 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65110.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 81.804; most accessible tissue: Zhenshan97 flower, score: 95.612 |
| vg0137791320 (J) | chr01 | 37791320 | A | G | 94.40% | 0.00% | A -> G |
mr1158 (All); LR P-value: 1.43E-15;
mr1168 (All); LR P-value: 2.00E-22; mr1244 (All); LR P-value: 9.11E-22; mr1415 (All); LR P-value: 3.06E-07; mr1465 (All); LR P-value: 1.74E-08; mr1550 (All); LR P-value: 1.44E-43; mr1567 (All); LR P-value: 3.06E-07; mr1612 (All); LR P-value: 9.36E-12; mr1757 (All); LR P-value: 5.88E-38; mr1931 (All); LR P-value: 2.23E-06; mr1510_2 (All); LR P-value: 3.55E-08; mr1530_2 (All); LR P-value: 8.28E-15; mr1549_2 (All); LR P-value: 5.23E-33; mr1550_2 (All); LR P-value: 5.32E-51; mr1757_2 (All); LR P-value: 9.62E-28 |
LOC_Os01g65100.3 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65110.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.718; most accessible tissue: Zhenshan97 flower, score: 95.646 |
| vg0137791385 (J) | chr01 | 37791385 | T | C | 58.50% | 0.06% | T -> C |
mr1003 (All); LR P-value: 6.22E-21;
mr1170 (All); LR P-value: 2.06E-12; mr1375 (All); LMM P-value: 9.02E-07; mr1375 (Ind_All); LMM P-value: 2.33E-06; LR P-value: 2.03E-08; mr1517 (All); LMM P-value: 5.28E-17; mr1517 (Ind_All); LMM P-value: 3.38E-15; LR P-value: 5.32E-19; mr1538 (All); LMM P-value: 6.51E-15; LR P-value: 3.22E-70; mr1538 (Ind_All); LMM P-value: 1.66E-11; LR P-value: 2.54E-14; mr1517_2 (All); LMM P-value: 4.14E-21; mr1517_2 (Ind_All); LMM P-value: 1.03E-19; LR P-value: 4.00E-22; mr1538_2 (All); LMM P-value: 3.91E-16; mr1538_2 (Ind_All); LMM P-value: 1.20E-13; LR P-value: 2.58E-20 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g65100.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65110.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.494; most accessible tissue: Zhenshan97 flower, score: 95.998 |
| vg0137791521 (J) | chr01 | 37791521 | G | T | 82.60% | 0.04% | G -> T |
mr1375 (Ind_All); LR P-value: 2.36E-06;
mr1517 (All); LMM P-value: 4.44E-09; mr1517 (Ind_All); LMM P-value: 8.35E-13; LR P-value: 4.48E-15; mr1538 (All); LMM P-value: 1.74E-08; mr1538 (Ind_All); LMM P-value: 7.98E-11; LR P-value: 3.12E-13; mr1517_2 (All); LMM P-value: 1.35E-09; mr1517_2 (Ind_All); LMM P-value: 1.75E-15; LR P-value: 1.15E-15; mr1538_2 (All); LMM P-value: 6.38E-08; mr1538_2 (Ind_All); LMM P-value: 1.57E-11; LR P-value: 1.18E-16 |
LOC_Os01g65100.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g65100.3 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os01g65100.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os01g65100.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g65100.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g65100.2 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.644; most accessible tissue: Zhenshan97 flower, score: 96.934 |
| vg0137791533 (J) | chr01 | 37791533 | G | A | 94.40% | 0.00% | G -> A |
mr1158 (All); LR P-value: 1.43E-15;
mr1168 (All); LR P-value: 2.00E-22; mr1244 (All); LR P-value: 9.11E-22; mr1415 (All); LR P-value: 3.06E-07; mr1465 (All); LR P-value: 1.74E-08; mr1550 (All); LR P-value: 1.44E-43; mr1567 (All); LR P-value: 3.06E-07; mr1612 (All); LR P-value: 9.36E-12; mr1757 (All); LR P-value: 5.88E-38; mr1931 (All); LR P-value: 2.23E-06; mr1510_2 (All); LR P-value: 3.55E-08; mr1530_2 (All); LR P-value: 8.28E-15; mr1549_2 (All); LR P-value: 5.23E-33; mr1550_2 (All); LR P-value: 5.32E-51; mr1757_2 (All); LR P-value: 9.62E-28 |
LOC_Os01g65100.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g65100.3 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os01g65100.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 87.879; most accessible tissue: Zhenshan97 flower, score: 96.969 |
| vg0137791764 (J) | chr01 | 37791764 | C | A | 58.60% | 0.06% | C -> A |
mr1170 (All); LR P-value: 1.12E-12;
mr1375 (All); LMM P-value: 2.99E-06; mr1375 (Ind_All); LR P-value: 7.71E-08; mr1517 (All); LMM P-value: 1.55E-17; mr1517 (Ind_All); LMM P-value: 2.77E-15; LR P-value: 1.16E-18; mr1538 (All); LMM P-value: 1.46E-14; LR P-value: 1.01E-69; mr1538 (Ind_All); LMM P-value: 1.22E-10; LR P-value: 1.48E-13; mr1517_2 (All); LMM P-value: 5.37E-21; mr1517_2 (Ind_All); LMM P-value: 5.16E-19; LR P-value: 3.18E-21; mr1538_2 (All); LMM P-value: 3.99E-16; mr1538_2 (Ind_All); LMM P-value: 2.72E-13; LR P-value: 8.87E-20 |
LOC_Os01g65100.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g65100.3 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os01g65100.2 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os01g65100.3 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g65100.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g65100.2 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 84.264; most accessible tissue: Zhenshan97 flower, score: 96.107 |
| vg0137791873 (J) | chr01 | 37791873 | G | A | 94.40% | 0.00% | G -> A |
mr1158 (All); LR P-value: 1.43E-15;
mr1168 (All); LR P-value: 2.00E-22; mr1244 (All); LR P-value: 9.11E-22; mr1415 (All); LR P-value: 3.06E-07; mr1465 (All); LR P-value: 1.74E-08; mr1550 (All); LR P-value: 1.44E-43; mr1567 (All); LR P-value: 3.06E-07; mr1612 (All); LR P-value: 9.36E-12; mr1757 (All); LR P-value: 5.88E-38; mr1931 (All); LR P-value: 2.23E-06; mr1510_2 (All); LR P-value: 3.55E-08; mr1530_2 (All); LR P-value: 8.28E-15; mr1549_2 (All); LR P-value: 5.23E-33; mr1550_2 (All); LR P-value: 5.32E-51; mr1757_2 (All); LR P-value: 9.62E-28 |
LOC_Os01g65100.1 Alt: A| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g65100.3 Alt: A| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os01g65100.2 Alt: A| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 83.348; most accessible tissue: Zhenshan97 flower, score: 96.634 |
| vg0137791880 (J) | chr01 | 37791880 | C | T | 59.00% | 0.00% | T -> C |
Yield (All); LR P-value: 1.09E-18;
mr1003 (All); LR P-value: 4.38E-22; mr1051 (All); LR P-value: 2.84E-22; mr1125 (All); LR P-value: 5.12E-48; mr1517 (All); LMM P-value: 2.11E-08; LR P-value: 6.02E-89; mr1538 (All); LMM P-value: 1.52E-07; LR P-value: 3.72E-80; mr1541 (All); LR P-value: 1.20E-20; mr1592 (All); LR P-value: 1.19E-14; mr1657 (All); LR P-value: 2.67E-11; mr1737 (All); LR P-value: 4.08E-33; mr1751 (All); LR P-value: 6.86E-11; mr1793 (All); LR P-value: 4.96E-29; mr1051_2 (All); LR P-value: 1.39E-26; mr1151_2 (All); LR P-value: 1.30E-12; mr1198_2 (All); LR P-value: 5.48E-09; mr1323_2 (All); LR P-value: 3.78E-26; mr1401_2 (All); LR P-value: 1.43E-21; mr1509_2 (All); LR P-value: 6.62E-44; mr1517_2 (All); LMM P-value: 1.08E-10; mr1538_2 (All); LMM P-value: 7.83E-09; mr1558_2 (All); LR P-value: 2.69E-56; mr1571_2 (All); LR P-value: 6.24E-33; mr1670_2 (All); LMM P-value: 3.25E-06; mr1793_2 (All); LR P-value: 9.98E-45; mr1885_2 (All); LR P-value: 2.19E-07; mr1922_2 (All); LR P-value: 4.74E-20; mr1924_2 (All); LR P-value: 1.42E-20 |
LOC_Os01g65100.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os01g65100.3 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os01g65110.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.786; most accessible tissue: Zhenshan97 flower, score: 96.524 |
| vg0137791924 (J) | chr01 | 37791924 | AT | ATT | 94.00% | 0.13% | AT -> CT,TT,ATT, A | NA |
LOC_Os01g65110.1 Alt: TT| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g65100.1 Alt: TT| intron_variant MODIFIER(snpEff) LOC_Os01g65100.3 Alt: TT| intron_variant MODIFIER(snpEff) LOC_Os01g65100.2 Alt: TT| intron_variant MODIFIER(snpEff) LOC_Os01g65110.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65110.1 Alt: ATT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.1 Alt: ATT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: ATT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: ATT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g65110.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g65100.1 Alt: CT| intron_variant MODIFIER(snpEff) LOC_Os01g65100.3 Alt: CT| intron_variant MODIFIER(snpEff) LOC_Os01g65100.2 Alt: CT| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.756; most accessible tissue: Zhenshan97 flower, score: 96.077 |
| vg0137791931 (J) | chr01 | 37791931 | T | Unkown | 96.40% | 2.29% | T -> TTTG | NA |
LOC_Os01g65110.1 Alt: TTTG| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g65100.1 Alt: TTTG| intron_variant MODIFIER(snpEff) LOC_Os01g65100.3 Alt: TTTG| intron_variant MODIFIER(snpEff) LOC_Os01g65100.2 Alt: TTTG| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.473; most accessible tissue: Zhenshan97 flower, score: 96.057 |
| vg0137791937 (J) | chr01 | 37791937 | A | G | 95.80% | 3.24% | A -> G | NA |
LOC_Os01g65110.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65100.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.851; most accessible tissue: Zhenshan97 flower, score: 96.067 |
| vg0137791944 (J) | chr01 | 37791944 | G | A | 98.10% | 0.00% | G -> A | NA |
LOC_Os01g65110.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g65100.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.3 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g65100.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.352; most accessible tissue: Zhenshan97 flower, score: 96.264 |
| vg0137791957 (J) | chr01 | 37791957 | C | Unkown | 95.80% | 3.24% | C -> T | NA |
LOC_Os01g65100.1 Alt: T| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os01g65100.3 Alt: T| splice_region_variant&intron_variant LOW(snpEff) LOC_Os01g65100.2 Alt: T| splice_region_variant&intron_variant LOW(snpEff) LOC_Os01g65110.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 84.129; most accessible tissue: Zhenshan97 flower, score: 96.107 |
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