128 variations found. LOC_Os01g60280 (ATP binding protein; putative; expressed), ranging from 34,868,403 bp to 34,879,449 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0134871033 (J) | chr01 | 34871033 | AA | AAA | 59.60% | 0.00% | AAA -> AA | NA |
|
| STR0134871506 (J) | chr01 | 34871506 | ATATATG TTTCC | ATATATA TTTCC | 54.80% | 0.00% | ATATATATTT CC -> ATATATGTTT CC,ATATATA TTTCT | NA |
|
| vg0134868423 (J) | chr01 | 34868423 | A | C | 63.90% | 0.00% | C -> A | NA |
LOC_Os01g60280.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60270.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.462; most accessible tissue: Minghui63 young leaf, score: 93.844 |
| vg0134868507 (J) | chr01 | 34868507 | TA | T | 61.50% | 0.00% | T -> TA | NA |
LOC_Os01g60280.1 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60270.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60270.2 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 85.310; most accessible tissue: Callus, score: 96.085 |
| vg0134868607 (J) | chr01 | 34868607 | C | CCACT | 99.00% | 0.00% | C -> CCACT | NA |
LOC_Os01g60280.1 Alt: CCACT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60270.1 Alt: CCACT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60270.2 Alt: CCACT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.904; most accessible tissue: Minghui63 young leaf, score: 96.366 |
| vg0134868702 (J) | chr01 | 34868702 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os01g60280.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os01g60270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g60270.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.421; most accessible tissue: Minghui63 young leaf, score: 96.859 |
| vg0134868711 (J) | chr01 | 34868711 | GA | GAA | 83.70% | 0.00% | GA -> GAA,G | NA |
LOC_Os01g60280.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60270.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60280.1 Alt: GAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60270.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60270.2 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.248; most accessible tissue: Minghui63 young leaf, score: 96.882 |
| vg0134868885 (J) | chr01 | 34868885 | G | A | 97.90% | 0.00% | G -> A | NA |
LOC_Os01g60280.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.988; most accessible tissue: Minghui63 young leaf, score: 97.240 |
| vg0134869178 (J) | chr01 | 34869178 | T | C | 98.90% | 0.00% | T -> C | NA |
LOC_Os01g60270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60270.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60280.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.618; most accessible tissue: Minghui63 young leaf, score: 95.412 |
| vg0134869211 (J) | chr01 | 34869211 | A | G | 98.90% | 0.00% | A -> G | NA |
LOC_Os01g60270.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60270.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60280.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 88.241; most accessible tissue: Minghui63 young leaf, score: 94.940 |
| vg0134869301 (J) | chr01 | 34869301 | G | A | 99.00% | 0.00% | G -> A | NA |
LOC_Os01g60280.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.588; most accessible tissue: Minghui63 young leaf, score: 93.881 |
| vg0134869410 (J) | chr01 | 34869410 | C | T | 97.90% | 0.00% | C -> T | NA |
LOC_Os01g60270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60270.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60280.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.230; most accessible tissue: Minghui63 young leaf, score: 93.073 |
| vg0134869507 (J) | chr01 | 34869507 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os01g60280.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os01g60270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g60270.2 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 88.657; most accessible tissue: Minghui63 young leaf, score: 92.927 |
| vg0134869693 (J) | chr01 | 34869693 | A | C | 99.90% | 0.00% | A -> C | NA |
LOC_Os01g60280.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os01g60270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g60270.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.896; most accessible tissue: Minghui63 root, score: 90.280 |
| vg0134869768 (J) | chr01 | 34869768 | C | T | 89.80% | 0.00% | C -> T | NA |
LOC_Os01g60270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60270.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60280.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.300; most accessible tissue: Minghui63 root, score: 89.689 |
| vg0134869876 (J) | chr01 | 34869876 | G | A | 96.80% | 0.00% | G -> A | NA |
LOC_Os01g60270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60270.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60280.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.919; most accessible tissue: Minghui63 root, score: 89.131 |
| vg0134869877 (J) | chr01 | 34869877 | C | T | 96.80% | 0.00% | C -> T | NA |
LOC_Os01g60270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60270.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60280.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.919; most accessible tissue: Minghui63 root, score: 89.131 |
| vg0134869973 (J) | chr01 | 34869973 | G | A | 53.10% | 0.00% | A -> G |
mr1003 (All); LR P-value: 5.72E-24;
mr1008 (All); LMM P-value: 6.14E-06; mr1008 (Ind_All); LMM P-value: 5.28E-07; LR P-value: 5.98E-08; mr1009 (All); LMM P-value: 5.38E-06; mr1009 (Ind_All); LMM P-value: 3.28E-07; LR P-value: 1.07E-07; mr1051 (All); LR P-value: 9.62E-25; mr1179 (All); LR P-value: 3.06E-18; mr1208 (All); LR P-value: 1.02E-31; mr1270 (All); LR P-value: 3.38E-13; mr1583 (All); LR P-value: 9.49E-16; mr1793 (All); LR P-value: 5.22E-28; mr1883 (All); LR P-value: 2.67E-12; mr1008_2 (Ind_All); LMM P-value: 5.95E-08; LR P-value: 4.89E-08; mr1051_2 (All); LR P-value: 2.52E-28; mr1151_2 (All); LR P-value: 4.45E-12; mr1164_2 (All); LR P-value: 1.27E-20; mr1189_2 (All); LR P-value: 3.03E-12; mr1221_2 (All); LR P-value: 3.11E-34; mr1244_2 (All); LR P-value: 1.88E-26; mr1422_2 (All); LR P-value: 2.36E-23; mr1744_2 (All); LR P-value: 3.75E-15; mr1850_2 (All); LR P-value: 5.51E-11; mr1932_2 (All); LR P-value: 1.16E-33 |
LOC_Os01g60280.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 69.682; most accessible tissue: Minghui63 root, score: 83.939 |
| vg0134869976 (J) | chr01 | 34869976 | C | T | 91.50% | 0.00% | C -> T |
LOC_Os01g60280.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 70.702; most accessible tissue: Minghui63 root, score: 84.069 |
|
| vg0134870086 (J) | chr01 | 34870086 | G | C | 99.90% | 0.00% | G -> C | NA |
LOC_Os01g60270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g60270.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g60280.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 67.964; most accessible tissue: Minghui63 flower, score: 83.608 |
| vg0134870545 (J) | chr01 | 34870545 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os01g60270.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g60270.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g60280.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 64.810; most accessible tissue: Callus, score: 88.439 |
| vg0134870775 (J) | chr01 | 34870775 | C | T | 99.50% | 0.00% | C -> T | NA |
LOC_Os01g60280.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 65.025; most accessible tissue: Callus, score: 86.793 |
| vg0134870797 (J) | chr01 | 34870797 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os01g60280.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os01g60270.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g60270.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 65.054; most accessible tissue: Callus, score: 86.793 |
| vg0134870908 (J) | chr01 | 34870908 | G | A | 55.60% | 0.00% | G -> A |
mr1003 (All); LR P-value: 2.55E-25;
mr1003 (Ind_All); LR P-value: 1.38E-06; mr1008 (Ind_All); LR P-value: 3.67E-06; mr1051 (All); LR P-value: 8.49E-25; mr1051 (Ind_All); LR P-value: 4.66E-06; mr1244 (All); LR P-value: 8.90E-21; mr1457 (All); LR P-value: 9.15E-09; mr1527 (All); LR P-value: 2.06E-06; mr1727 (All); LR P-value: 6.26E-07; mr1887 (Ind_All); LR P-value: 5.33E-06; mr1008_2 (Ind_All); LMM P-value: 5.38E-06; LR P-value: 2.10E-07; mr1027_2 (Ind_All); LR P-value: 5.21E-08; mr1051_2 (All); LR P-value: 9.54E-27; mr1051_2 (Ind_All); LR P-value: 4.45E-06; mr1218_2 (All); LR P-value: 8.11E-19; mr1244_2 (All); LR P-value: 1.93E-26; mr1583_2 (All); LR P-value: 3.95E-14; mr1850_2 (All); LR P-value: 3.42E-12 |
LOC_Os01g60280.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 61.582; most accessible tissue: Minghui63 flower, score: 80.659 |
| vg0134871022 (J) | chr01 | 34871022 | C | A | 95.30% | 0.00% | C -> A | NA |
LOC_Os01g60270.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g60270.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g60280.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 58.277; most accessible tissue: Minghui63 flower, score: 75.455 |
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