27 variations found. LOC_Os02g35760 (STRUBBELIG-RECEPTOR FAMILY 7 precursor; putative; expressed), ranging from 21,474,732 bp to 21,477,632 bp (including 0 kb upstream and 0 kb downstream of the gene).
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0221474880 (J) | chr02 | 21474880 | C | T | 57.00% | 0.00% | T -> C |
mr1156 (All); LR P-value: 6.26E-15;
mr1720 (All); LR P-value: 3.70E-10; mr1914 (All); LR P-value: 2.23E-12; mr1918 (Jap_All); LMM P-value: 6.03E-06; LR P-value: 6.03E-06; mr1109_2 (All); LR P-value: 1.67E-56; mr1509_2 (All); LR P-value: 2.57E-45; mr1514_2 (All); LR P-value: 8.05E-13; mr1720_2 (All); LR P-value: 2.50E-15; mr1911_2 (Jap_All); LR P-value: 5.62E-06 |
LOC_Os02g35760.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35750.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35740.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 53.875; most accessible tissue: Zhenshan97 young leaf, score: 68.315 |
| vg0221474956 (J) | chr02 | 21474956 | T | A | 99.80% | 0.00% | T -> A | NA |
LOC_Os02g35760.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g35750.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g35760.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g35740.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g35750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g35750.3 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.343; most accessible tissue: Callus, score: 84.947 |
| vg0221474990 (J) | chr02 | 21474990 | A | T | 96.00% | 0.00% | A -> T |
LOC_Os02g35760.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35750.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35740.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 51.599; most accessible tissue: Callus, score: 84.947 |
|
| vg0221475189 (J) | chr02 | 21475189 | C | T | 61.10% | 0.13% | T -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g35760.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35740.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.724; most accessible tissue: Callus, score: 86.199 |
|
| vg0221475357 (J) | chr02 | 21475357 | G | GA | 65.40% | 0.00% | GA -> G | NA |
LOC_Os02g35760.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g35760.2 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35740.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.979; most accessible tissue: Minghui63 flag leaf, score: 84.791 |
| vg0221475404 (J) | chr02 | 21475404 | C | T | 56.90% | 0.00% | T -> C |
mr1156 (All); LR P-value: 8.66E-15;
mr1720 (All); LR P-value: 3.53E-11; mr1756 (All); LR P-value: 1.17E-06; mr1914 (All); LR P-value: 3.38E-12; mr1918 (Jap_All); LMM P-value: 3.32E-06; LR P-value: 3.32E-06; mr1037_2 (All); LR P-value: 6.80E-31; mr1109_2 (All); LR P-value: 9.63E-58; mr1509_2 (All); LR P-value: 7.54E-45; mr1514_2 (All); LR P-value: 5.79E-13; mr1720_2 (All); LR P-value: 8.59E-16; mr1911_2 (Jap_All); LR P-value: 1.59E-06 |
LOC_Os02g35750.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35750.3 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35740.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.431; most accessible tissue: Minghui63 flower, score: 81.411 |
| vg0221475461 (J) | chr02 | 21475461 | G | A | 65.30% | 0.13% | A -> G |
mr1014 (All); LR P-value: 1.04E-71;
mr1027 (All); LR P-value: 1.99E-65; mr1128 (All); LR P-value: 4.10E-11; mr1134 (All); LR P-value: 5.55E-82; mr1135 (All); LR P-value: 3.34E-76; mr1375 (All); LR P-value: 1.72E-23; mr1504 (All); LR P-value: 7.86E-90; mr1514 (All); LR P-value: 7.36E-08; mr1670 (All); LR P-value: 1.10E-33; mr1672 (All); LR P-value: 2.53E-84; mr1682 (All); LR P-value: 7.16E-36; mr1695 (All); LR P-value: 7.88E-59; mr1714 (All); LR P-value: 1.11E-10; mr1754 (All); LR P-value: 2.46E-19; mr1767 (All); LR P-value: 4.00E-18; mr1918 (Jap_All); LMM P-value: 3.32E-06; LR P-value: 3.32E-06; mr1987 (All); LR P-value: 2.34E-100; mr1128_2 (All); LR P-value: 2.44E-12; mr1416_2 (All); LR P-value: 2.90E-17; mr1911_2 (Jap_All); LR P-value: 1.59E-06 |
LOC_Os02g35760.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35760.2 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os02g35760.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os02g35760.2 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 64.351; most accessible tissue: Callus, score: 83.659 |
| vg0221475627 (J) | chr02 | 21475627 | A | C | 65.30% | 0.11% | C -> A |
mr1014 (All); LR P-value: 1.04E-71;
mr1027 (All); LR P-value: 1.99E-65; mr1128 (All); LR P-value: 4.10E-11; mr1134 (All); LR P-value: 5.55E-82; mr1135 (All); LR P-value: 3.34E-76; mr1375 (All); LR P-value: 1.72E-23; mr1504 (All); LR P-value: 7.86E-90; mr1514 (All); LR P-value: 7.36E-08; mr1670 (All); LR P-value: 1.10E-33; mr1672 (All); LR P-value: 2.53E-84; mr1682 (All); LR P-value: 7.16E-36; mr1695 (All); LR P-value: 7.88E-59; mr1714 (All); LR P-value: 1.11E-10; mr1754 (All); LR P-value: 2.46E-19; mr1767 (All); LR P-value: 4.00E-18; mr1918 (Jap_All); LMM P-value: 3.32E-06; LR P-value: 3.32E-06; mr1987 (All); LR P-value: 2.34E-100; mr1128_2 (All); LR P-value: 2.44E-12; mr1416_2 (All); LR P-value: 2.90E-17; mr1911_2 (Jap_All); LR P-value: 1.59E-06 |
LOC_Os02g35760.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os02g35760.2 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35740.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 68.464; most accessible tissue: Minghui63 flower, score: 78.041 |
| vg0221475737 (J) | chr02 | 21475737 | T | C | 65.40% | 0.00% | C -> T |
mr1014 (All); LR P-value: 1.04E-71;
mr1027 (All); LR P-value: 1.99E-65; mr1128 (All); LR P-value: 4.10E-11; mr1134 (All); LR P-value: 5.55E-82; mr1135 (All); LR P-value: 3.34E-76; mr1375 (All); LR P-value: 1.72E-23; mr1504 (All); LR P-value: 7.86E-90; mr1514 (All); LR P-value: 7.36E-08; mr1670 (All); LR P-value: 1.10E-33; mr1672 (All); LR P-value: 2.53E-84; mr1682 (All); LR P-value: 7.16E-36; mr1695 (All); LR P-value: 7.88E-59; mr1714 (All); LR P-value: 1.11E-10; mr1754 (All); LR P-value: 2.46E-19; mr1767 (All); LR P-value: 4.00E-18; mr1918 (Jap_All); LMM P-value: 3.32E-06; LR P-value: 3.32E-06; mr1987 (All); LR P-value: 2.34E-100; mr1128_2 (All); LR P-value: 2.44E-12; mr1416_2 (All); LR P-value: 2.90E-17; mr1911_2 (Jap_All); LR P-value: 1.59E-06 |
LOC_Os02g35760.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g35760.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 74.787; most accessible tissue: Callus, score: 85.683 |
| vg0221475833 (J) | chr02 | 21475833 | C | T | 56.90% | 0.13% | T -> C |
mr1156 (All); LR P-value: 7.65E-15;
mr1720 (All); LR P-value: 4.75E-11; mr1914 (All); LR P-value: 1.74E-12; mr1918 (Jap_All); LMM P-value: 3.32E-06; LR P-value: 3.32E-06; mr1037_2 (All); LR P-value: 1.53E-30; mr1109_2 (All); LR P-value: 1.22E-56; mr1509_2 (All); LR P-value: 1.68E-44; mr1514_2 (All); LR P-value: 5.77E-13; mr1720_2 (All); LR P-value: 5.75E-16; mr1911_2 (Jap_All); LR P-value: 1.59E-06 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g35740.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.003; most accessible tissue: Zhenshan97 flag leaf, score: 84.585 |
| vg0221475862 (J) | chr02 | 21475862 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os02g35740.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g35750.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g35750.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g35750.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g35760.1 Alt: C| intron_variant MODIFIER(snpEff) LOC_Os02g35760.2 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 76.119; most accessible tissue: Zhenshan97 flag leaf, score: 85.761 |
| vg0221475954 (J) | chr02 | 21475954 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os02g35760.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os02g35760.2 Alt: A| synonymous_variant LOW(snpEff) LOC_Os02g35740.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g35750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g35750.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g35750.3 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.666; most accessible tissue: Zhenshan97 flag leaf, score: 87.567 |
| vg0221476188 (J) | chr02 | 21476188 | C | T | 65.30% | 0.08% | T -> C |
mr1014 (All); LR P-value: 1.04E-71;
mr1027 (All); LR P-value: 1.99E-65; mr1128 (All); LR P-value: 4.10E-11; mr1134 (All); LR P-value: 5.55E-82; mr1135 (All); LR P-value: 3.34E-76; mr1375 (All); LR P-value: 1.72E-23; mr1504 (All); LR P-value: 7.86E-90; mr1514 (All); LR P-value: 7.36E-08; mr1670 (All); LR P-value: 1.10E-33; mr1672 (All); LR P-value: 2.53E-84; mr1682 (All); LR P-value: 7.16E-36; mr1695 (All); LR P-value: 7.88E-59; mr1714 (All); LR P-value: 1.11E-10; mr1754 (All); LR P-value: 2.46E-19; mr1767 (All); LR P-value: 4.00E-18; mr1918 (Jap_All); LMM P-value: 3.32E-06; LR P-value: 3.32E-06; mr1987 (All); LR P-value: 2.34E-100; mr1128_2 (All); LR P-value: 2.44E-12; mr1416_2 (All); LR P-value: 2.90E-17; mr1911_2 (Jap_All); LR P-value: 1.59E-06 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g35750.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 77.021; most accessible tissue: Zhenshan97 flag leaf, score: 82.703 |
| vg0221476200 (J) | chr02 | 21476200 | C | T | 65.30% | 0.08% | T -> C |
mr1014 (All); LR P-value: 8.46E-72;
mr1027 (All); LR P-value: 1.79E-65; mr1074 (All); LR P-value: 7.83E-31; mr1128 (All); LR P-value: 5.34E-11; mr1134 (All); LR P-value: 8.84E-82; mr1135 (All); LR P-value: 1.33E-75; mr1375 (All); LR P-value: 7.53E-24; mr1504 (All); LR P-value: 6.00E-90; mr1514 (All); LR P-value: 2.67E-08; mr1632 (All); LR P-value: 4.07E-26; mr1670 (All); LR P-value: 8.28E-34; mr1672 (All); LR P-value: 1.92E-83; mr1682 (All); LR P-value: 2.42E-35; mr1695 (All); LR P-value: 6.50E-59; mr1714 (All); LR P-value: 5.98E-11; mr1767 (All); LR P-value: 5.29E-18; mr1918 (Jap_All); LMM P-value: 3.32E-06; LR P-value: 3.32E-06; mr1987 (All); LR P-value: 3.94E-99; mr1416_2 (All); LR P-value: 3.84E-17; mr1911_2 (Jap_All); LR P-value: 1.59E-06; mr1947_2 (All); LR P-value: 5.65E-09 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g35750.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 76.588; most accessible tissue: Zhenshan97 flag leaf, score: 82.874 |
| vg0221476316 (J) | chr02 | 21476316 | C | T | 65.30% | 0.08% | T -> C |
mr1014 (All); LR P-value: 1.04E-71;
mr1027 (All); LR P-value: 1.99E-65; mr1128 (All); LR P-value: 4.10E-11; mr1134 (All); LR P-value: 5.55E-82; mr1135 (All); LR P-value: 3.34E-76; mr1375 (All); LR P-value: 1.72E-23; mr1504 (All); LR P-value: 7.86E-90; mr1514 (All); LR P-value: 7.36E-08; mr1670 (All); LR P-value: 1.10E-33; mr1672 (All); LR P-value: 2.53E-84; mr1682 (All); LR P-value: 7.16E-36; mr1695 (All); LR P-value: 7.88E-59; mr1714 (All); LR P-value: 1.11E-10; mr1754 (All); LR P-value: 2.46E-19; mr1767 (All); LR P-value: 4.00E-18; mr1918 (Jap_All); LMM P-value: 3.32E-06; LR P-value: 3.32E-06; mr1987 (All); LR P-value: 2.34E-100; mr1128_2 (All); LR P-value: 2.44E-12; mr1416_2 (All); LR P-value: 2.90E-17; mr1911_2 (Jap_All); LR P-value: 1.59E-06 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g35750.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.951; most accessible tissue: Callus, score: 81.857 |
| vg0221476344 (J) | chr02 | 21476344 | GCTGTAG TTCGTTG AGTAATG A | G | 95.90% | 0.00% | GCTGTAGTTC GTTGAGTAAT GA -> G | NA |
LOC_Os02g35750.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35750.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.018; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 |
| vg0221476579 (J) | chr02 | 21476579 | A | G | 95.80% | 0.00% | A -> G | NA |
LOC_Os02g35750.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35750.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.234; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 |
| vg0221476621 (J) | chr02 | 21476621 | GGAA | G | 60.10% | 0.06% | G -> GGAA,A | NA |
LOC_Os02g35750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35750.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.1 Alt: GGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: GGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: GGAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.1 Alt: GGAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: GGAA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 71.019; most accessible tissue: Zhenshan97 young leaf, score: 83.412 |
| vg0221477121 (J) | chr02 | 21477121 | TTCC | T | 64.50% | 0.00% | T -> TTCC,C | NA |
LOC_Os02g35760.1 Alt: TTCC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35760.2 Alt: TTCC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.1 Alt: TTCC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: TTCC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: TTCC| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.383; most accessible tissue: Zhenshan97 flag leaf, score: 81.605 |
| vg0221477230 (J) | chr02 | 21477230 | G | A | 99.20% | 0.00% | G -> A | NA |
LOC_Os02g35760.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.395; most accessible tissue: Zhenshan97 flag leaf, score: 79.481 |
| vg0221477243 (J) | chr02 | 21477243 | C | A | 99.10% | 0.00% | C -> A | NA |
LOC_Os02g35760.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.191; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 |
| vg0221477301 (J) | chr02 | 21477301 | G | GA | 61.10% | 0.00% | GA -> G | NA |
LOC_Os02g35750.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35750.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.288; most accessible tissue: Zhenshan97 flag leaf, score: 74.825 |
| vg0221477426 (J) | chr02 | 21477426 | C | G | 65.30% | 0.02% | G -> C,T |
mr1014 (All); LR P-value: 1.04E-71;
mr1027 (All); LR P-value: 1.99E-65; mr1128 (All); LR P-value: 4.10E-11; mr1134 (All); LR P-value: 5.55E-82; mr1135 (All); LR P-value: 3.34E-76; mr1375 (All); LR P-value: 1.72E-23; mr1504 (All); LR P-value: 7.86E-90; mr1514 (All); LR P-value: 7.36E-08; mr1670 (All); LR P-value: 1.10E-33; mr1672 (All); LR P-value: 2.53E-84; mr1682 (All); LR P-value: 7.16E-36; mr1695 (All); LR P-value: 7.88E-59; mr1714 (All); LR P-value: 1.11E-10; mr1754 (All); LR P-value: 2.46E-19; mr1767 (All); LR P-value: 4.00E-18; mr1918 (Jap_All); LMM P-value: 3.32E-06; LR P-value: 3.32E-06; mr1987 (All); LR P-value: 2.34E-100; mr1128_2 (All); LR P-value: 2.44E-12; mr1416_2 (All); LR P-value: 2.90E-17; mr1911_2 (Jap_All); LR P-value: 1.59E-06 |
LOC_Os02g35750.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35750.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os02g35750.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35760.2 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 72.380; most accessible tissue: Callus, score: 89.453 |
| vg0221477552 (J) | chr02 | 21477552 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os02g35760.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g35760.2 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g35750.3 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.594; most accessible tissue: Callus, score: 89.453 |
| STR0221475358 (J) | chr02 | 21475358 | AAA | AAAA | 64.10% | 0.00% | AAAA -> AAA | NA |
|
| STR0221476574 (J) | chr02 | 21476574 | AGATGAA GATGAGC A | AGATGGA GATGAGC A | 98.20% | 0.00% | AGATGAAGAT GAGCA -> AGATGGAGAT GAGCA | NA |
|
| STR0221476622 (J) | chr02 | 21476622 | GAAGAAG | GAAG | 59.70% | 0.00% | GAAG -> GAAGAAG | NA |
|