25 variations found. LOC_Os02g47190 (MYB family transcription factor; putative; expressed), ranging from 28,808,919 bp to 28,811,976 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0228808982 (J) | chr02 | 28808982 | CCT | CCTCT | 94.20% | 0.00% | CCT -> CCTCTCT,CC TCT,C | NA |
LOC_Os02g47190.1 Alt: CCTCT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47180.1 Alt: CCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47200.1 Alt: CCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47180.2 Alt: CCTCT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47190.1 Alt: CCTCTCT| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g47180.1 Alt: CCTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47200.1 Alt: CCTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47180.2 Alt: CCTCTCT| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47190.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g47180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47200.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47180.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 97.593; most accessible tissue: Minghui63 flag leaf, score: 99.642 |
| vg0228809031 (J) | chr02 | 28809031 | C | T | 97.40% | 0.00% | C -> T | NA |
LOC_Os02g47190.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47180.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.134; most accessible tissue: Minghui63 flag leaf, score: 99.594 |
| vg0228809054 (J) | chr02 | 28809054 | CTG | C | 97.40% | 0.00% | CTG -> C,GTG | NA |
LOC_Os02g47190.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47180.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47200.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47180.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47190.1 Alt: GTG| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os02g47190.1 Alt: GTG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47180.1 Alt: GTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47200.1 Alt: GTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47180.2 Alt: GTG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.008; most accessible tissue: Minghui63 flag leaf, score: 99.576 |
| vg0228809226 (J) | chr02 | 28809226 | G | A | 94.50% | 0.00% | G -> A |
mr1076 (Jap_All); LR P-value: 1.56E-08;
mr1082 (Jap_All); LR P-value: 6.60E-08; mr1083 (Jap_All); LR P-value: 4.06E-07; mr1086 (Jap_All); LR P-value: 7.03E-06; mr1103 (Jap_All); LR P-value: 2.61E-06; mr1226 (Jap_All); LR P-value: 4.71E-09; mr1227 (Jap_All); LR P-value: 4.93E-07; mr1411 (Jap_All); LR P-value: 1.34E-06; mr1152_2 (Jap_All); LR P-value: 4.09E-06; mr1226_2 (Jap_All); LR P-value: 5.62E-07 |
LOC_Os02g47190.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47180.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47180.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 94.101; most accessible tissue: Minghui63 flag leaf, score: 99.180 |
| vg0228809292 (J) | chr02 | 28809292 | TC | T | 94.50% | 0.00% | TC -> T | NA |
LOC_Os02g47190.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47180.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.182; most accessible tissue: Minghui63 flag leaf, score: 98.905 |
| vg0228809977 (J) | chr02 | 28809977 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os02g47190.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 76.699; most accessible tissue: Minghui63 flag leaf, score: 94.967 |
| vg0228810047 (J) | chr02 | 28810047 | CT | C | 52.80% | 0.28% | C -> CT | NA |
LOC_Os02g47180.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47200.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47180.2 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47190.1 Alt: CT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.308; most accessible tissue: Minghui63 flag leaf, score: 95.135 |
| vg0228810340 (J) | chr02 | 28810340 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os02g47190.1 Alt: A| splice_acceptor_variant&intron_variant HIGH(snpEff)/splice_acceptor_variant(CooVar)
The average chromatin accessibility score: 70.518; most accessible tissue: Minghui63 flag leaf, score: 92.416 |
| vg0228810544 (J) | chr02 | 28810544 | T | C | 53.20% | 0.47% | C -> T |
LOC_Os02g47180.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47180.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47190.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 80.469; most accessible tissue: Minghui63 flag leaf, score: 92.011 |
|
| vg0228810572 (J) | chr02 | 28810572 | A | AG | 99.60% | 0.00% | A -> AG,AAGGGG | NA |
LOC_Os02g47180.1 Alt: AG| downstream_gene_variant MODIFIER(snpEff)
LOC_Os02g47200.1 Alt: AG| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47210.1 Alt: AG| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47180.2 Alt: AG| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47190.1 Alt: AG| intron_variant MODIFIER(snpEff) LOC_Os02g47180.1 Alt: AAGGGG| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47200.1 Alt: AAGGGG| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47210.1 Alt: AAGGGG| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47180.2 Alt: AAGGGG| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47190.1 Alt: AAGGGG| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 82.362; most accessible tissue: Zhenshan97 root, score: 92.946 |
| vg0228810638 (J) | chr02 | 28810638 | G | A | 94.50% | 0.00% | G -> A |
mr1076 (Jap_All); LR P-value: 1.56E-08;
mr1082 (Jap_All); LR P-value: 6.60E-08; mr1083 (Jap_All); LR P-value: 4.06E-07; mr1086 (Jap_All); LR P-value: 7.03E-06; mr1103 (Jap_All); LR P-value: 2.61E-06; mr1226 (Jap_All); LR P-value: 4.71E-09; mr1227 (Jap_All); LR P-value: 4.93E-07; mr1411 (Jap_All); LR P-value: 1.34E-06; mr1152_2 (Jap_All); LR P-value: 4.09E-06; mr1226_2 (Jap_All); LR P-value: 5.62E-07 |
LOC_Os02g47180.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47180.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47190.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.371; most accessible tissue: Zhenshan97 root, score: 94.011 |
| vg0228810846 (J) | chr02 | 28810846 | TA | T | 52.90% | 0.49% | T -> TA | NA |
LOC_Os02g47180.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47200.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47210.1 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47180.2 Alt: TA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47190.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.179; most accessible tissue: Zhenshan97 root, score: 92.883 |
| vg0228810943 (J) | chr02 | 28810943 | T | A | 94.50% | 0.00% | T -> A |
mr1076 (Jap_All); LR P-value: 1.56E-08;
mr1082 (Jap_All); LR P-value: 6.60E-08; mr1083 (Jap_All); LR P-value: 4.06E-07; mr1086 (Jap_All); LR P-value: 7.03E-06; mr1103 (Jap_All); LR P-value: 2.61E-06; mr1226 (Jap_All); LR P-value: 4.71E-09; mr1227 (Jap_All); LR P-value: 4.93E-07; mr1411 (Jap_All); LR P-value: 1.34E-06; mr1152_2 (Jap_All); LR P-value: 4.09E-06; mr1226_2 (Jap_All); LR P-value: 5.62E-07 |
LOC_Os02g47180.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47180.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47190.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.229; most accessible tissue: Minghui63 flag leaf, score: 91.625 |
| vg0228811150 (J) | chr02 | 28811150 | T | A | 65.50% | 0.47% | T -> A | NA |
LOC_Os02g47200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47190.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 69.338; most accessible tissue: Minghui63 flag leaf, score: 92.689 |
| vg0228811181 (J) | chr02 | 28811181 | T | C | 53.20% | 0.00% | C -> T,G |
LOC_Os02g47190.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os02g47200.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47210.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g47190.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 73.405; most accessible tissue: Minghui63 flag leaf, score: 93.043 |
|
| vg0228811254 (J) | chr02 | 28811254 | C | T | 58.40% | 0.55% | C -> T | NA |
LOC_Os02g47200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47190.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 75.403; most accessible tissue: Minghui63 flag leaf, score: 94.329 |
| vg0228811319 (J) | chr02 | 28811319 | G | A | 97.80% | 0.00% | G -> A | NA |
LOC_Os02g47200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47190.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 75.539; most accessible tissue: Minghui63 flag leaf, score: 93.957 |
| vg0228811504 (J) | chr02 | 28811504 | A | C | 98.40% | 0.00% | A -> C | NA |
LOC_Os02g47190.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 77.271; most accessible tissue: Minghui63 flag leaf, score: 95.215 |
| vg0228811687 (J) | chr02 | 28811687 | G | A | 52.90% | 0.08% | A -> G |
LOC_Os02g47190.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os02g47190.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 78.807; most accessible tissue: Minghui63 flag leaf, score: 94.996 |
|
| vg0228811875 (J) | chr02 | 28811875 | T | C | 99.80% | 0.00% | T -> C | NA |
LOC_Os02g47190.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47200.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.973; most accessible tissue: Minghui63 flag leaf, score: 95.189 |
| vg0228811883 (J) | chr02 | 28811883 | T | C | 65.50% | 0.47% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os02g47190.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47200.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.360; most accessible tissue: Minghui63 flag leaf, score: 95.321 |
| vg0228811941 (J) | chr02 | 28811941 | A | C | 52.80% | 0.47% | C -> A |
LOC_Os02g47190.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47200.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 79.287; most accessible tissue: Minghui63 flag leaf, score: 94.939 |
|
| vg0228811952 (J) | chr02 | 28811952 | T | C | 53.10% | 0.49% | C -> T |
LOC_Os02g47190.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 78.833; most accessible tissue: Minghui63 flag leaf, score: 95.052 |
|
| vg0228811970 (J) | chr02 | 28811970 | A | G | 98.40% | 0.00% | A -> G,T | NA |
LOC_Os02g47190.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g47200.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47210.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47190.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47200.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g47210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 78.929; most accessible tissue: Minghui63 flag leaf, score: 95.215 |
| STR0228810943 (J) | chr02 | 28810943 | T | A | 96.30% | 0.00% | T -> A | NA |
|