29 variations found. LOC_Os01g38130 (expressed protein), ranging from 21,349,837 bp to 21,350,379 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0121349873 (J) | chr01 | 21349873 | AAAG | A | 99.20% | 0.00% | AAAG -> A | NA |
LOC_Os01g38130.1 Alt: A| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 84.881; most accessible tissue: Minghui63 root, score: 92.303 |
| vg0121349906 (J) | chr01 | 21349906 | C | G | 99.20% | 0.00% | C -> G | NA |
LOC_Os01g38130.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 83.045; most accessible tissue: Minghui63 root, score: 89.944 |
| vg0121349921 (J) | chr01 | 21349921 | C | T | 99.20% | 0.00% | C -> T | NA |
LOC_Os01g38130.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.739; most accessible tissue: Minghui63 root, score: 90.139 |
| vg0121349933 (J) | chr01 | 21349933 | C | G | 99.20% | 0.00% | C -> G | NA |
LOC_Os01g38130.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 84.072; most accessible tissue: Minghui63 root, score: 89.944 |
| vg0121349974 (J) | chr01 | 21349974 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os01g38130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 84.209; most accessible tissue: Minghui63 root, score: 88.953 |
| vg0121350039 (J) | chr01 | 21350039 | C | G | 99.20% | 0.00% | C -> G | NA |
LOC_Os01g38130.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 81.378; most accessible tissue: Minghui63 root, score: 85.870 |
| vg0121350046 (J) | chr01 | 21350046 | A | G | 99.20% | 0.00% | A -> G | NA |
LOC_Os01g38130.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 81.478; most accessible tissue: Minghui63 flag leaf, score: 85.670 |
| vg0121350108 (J) | chr01 | 21350108 | TG | T | 98.70% | 0.00% | TG -> T | NA |
LOC_Os01g38120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.691; most accessible tissue: Zhenshan97 root, score: 83.751 |
| vg0121350157 (J) | chr01 | 21350157 | C | T | 98.70% | 0.00% | C -> T | NA |
LOC_Os01g38120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.694; most accessible tissue: Zhenshan97 root, score: 80.208 |
| vg0121350166 (J) | chr01 | 21350166 | A | T | 98.70% | 0.00% | A -> T | NA |
LOC_Os01g38120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.236; most accessible tissue: Zhenshan97 root, score: 80.448 |
| vg0121350170 (J) | chr01 | 21350170 | C | G | 98.70% | 0.00% | C -> G | NA |
LOC_Os01g38120.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.666; most accessible tissue: Zhenshan97 root, score: 79.452 |
| vg0121350172 (J) | chr01 | 21350172 | TTCCGTC CTTATAT ATA | T | 98.70% | 0.00% | TTCCGTCCTT ATATATA -> T,TGATCCGT CCTTATATAT A | NA |
LOC_Os01g38120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38120.1 Alt: TGATCCGTCCTTATATATA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38140.1 Alt: TGATCCGTCCTTATATATA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: TGATCCGTCCTTATATATA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 67.912; most accessible tissue: Zhenshan97 root, score: 79.452 |
| vg0121350176 (J) | chr01 | 21350176 | G | A | 96.70% | 0.00% | G -> A | NA |
LOC_Os01g38120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.396; most accessible tissue: Callus, score: 80.173 |
| vg0121350184 (J) | chr01 | 21350184 | T | A | 54.70% | 0.00% | A -> T |
mr1047 (All); LR P-value: 5.88E-09;
mr1189 (All); LR P-value: 1.09E-06; mr1625 (All); LR P-value: 3.05E-06; mr1698 (All); LMM P-value: 2.78E-06; LR P-value: 2.54E-25; mr1698 (Ind_All); LR P-value: 4.89E-06; mr1782 (All); LR P-value: 8.35E-06; mr1796 (All); LR P-value: 9.62E-08; mr1990 (All); LR P-value: 1.66E-07; mr1698_2 (All); LR P-value: 1.97E-21; mr1925_2 (All); LR P-value: 2.91E-06 |
LOC_Os01g38120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 70.125; most accessible tissue: Callus, score: 80.173 |
| vg0121350190 (J) | chr01 | 21350190 | AT | A | 98.70% | 0.00% | AT -> A | NA |
LOC_Os01g38120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.517; most accessible tissue: Callus, score: 80.173 |
| vg0121350193 (J) | chr01 | 21350193 | CATT | C | 98.70% | 0.00% | CATT -> C | NA |
LOC_Os01g38120.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.711; most accessible tissue: Callus, score: 80.173 |
| vg0121350198 (J) | chr01 | 21350198 | G | A | 94.90% | 0.00% | G -> A |
LOC_Os01g38120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 68.338; most accessible tissue: Callus, score: 80.173 |
|
| vg0121350219 (J) | chr01 | 21350219 | C | T | 98.10% | 0.59% | C -> T | NA |
LOC_Os01g38120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 66.289; most accessible tissue: Callus, score: 80.173 |
| vg0121350221 (J) | chr01 | 21350221 | G | GT | 99.10% | 0.00% | G -> GT | NA |
LOC_Os01g38120.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: GT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: GT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 66.260; most accessible tissue: Callus, score: 80.173 |
| vg0121350228 (J) | chr01 | 21350228 | C | T | 98.70% | 0.00% | C -> T | NA |
LOC_Os01g38120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.197; most accessible tissue: Callus, score: 80.173 |
| vg0121350236 (J) | chr01 | 21350236 | G | A | 98.70% | 0.00% | G -> A | NA |
LOC_Os01g38120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 62.140; most accessible tissue: Callus, score: 80.173 |
| vg0121350269 (J) | chr01 | 21350269 | A | G | 98.70% | 0.00% | A -> G | NA |
LOC_Os01g38120.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.912; most accessible tissue: Callus, score: 80.173 |
| vg0121350291 (J) | chr01 | 21350291 | G | T | 98.70% | 0.00% | G -> T | NA |
LOC_Os01g38120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 57.072; most accessible tissue: Callus, score: 80.173 |
| vg0121350313 (J) | chr01 | 21350313 | T | A | 59.80% | 0.00% | A -> T | NA |
LOC_Os01g38120.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.318; most accessible tissue: Callus, score: 80.173 |
| vg0121350314 (J) | chr01 | 21350314 | T | A | 98.60% | 0.00% | T -> A | NA |
LOC_Os01g38120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.318; most accessible tissue: Callus, score: 80.173 |
| vg0121350315 (J) | chr01 | 21350315 | T | A | 98.70% | 0.00% | T -> A | NA |
LOC_Os01g38120.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g38140.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g38130.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 54.447; most accessible tissue: Callus, score: 80.173 |
| vg0121350362 (J) | chr01 | 21350362 | A | G | 98.70% | 0.00% | A -> G | NA |
LOC_Os01g38130.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 45.922; most accessible tissue: Minghui63 panicle, score: 68.460 |
| vg0121350364 (J) | chr01 | 21350364 | C | T | 98.70% | 0.00% | C -> T | NA |
LOC_Os01g38130.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 45.562; most accessible tissue: Minghui63 panicle, score: 68.460 |
| STR0121350175 (J) | chr01 | 21350175 | CGTCCTT ATT | CGTCCTT ATA | 50.00% | 0.00% | CGTCCTTATA -> CGTCCTTATT ,CATCCTTAT A | NA |
|