28 variations found. Os02g0187700/LOC_Os02g09480 (myb-like DNA-binding domain containing protein; putative; expressed), ranging from 4,867,673 bp to 4,869,380 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g09480 | myb-like DNA-binding domain containing protein, putative, expressed; RAP ID: Os02g0187700; MSU ID: LOC_Os02g09480 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0204867716 (J) | chr02 | 4867716 | A | AAGG | 97.10% | 0.00% | A -> AAGG | NA |
LOC_Os02g09480.1 Alt: AAGG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09470.1 Alt: AAGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09490.1 Alt: AAGG| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 99.744; most accessible tissue: Minghui63 young leaf, score: 99.942 |
| vg0204867998 (J) | chr02 | 4867998 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os02g09480.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 95.509; most accessible tissue: Minghui63 panicle, score: 99.545 |
| vg0204868292 (J) | chr02 | 4868292 | AACGACG ACGACGG CG | A | 79.70% | 0.21% | AACGACGACG ACGGCG -> A | NA |
LOC_Os02g09480.1 Alt: A| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os02g09480.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 93.958; most accessible tissue: Minghui63 panicle, score: 99.147 |
| vg0204868293 (J) | chr02 | 4868293 | ACGACGA CGACGG | A | 86.40% | 0.00% | ACGACGACGA CGG -> A | NA |
LOC_Os02g09480.1 Alt: A| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 93.964; most accessible tissue: Minghui63 panicle, score: 99.153 |
| vg0204868399 (J) | chr02 | 4868399 | C | T | 79.80% | 0.00% | C -> T | NA |
LOC_Os02g09480.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.399; most accessible tissue: Minghui63 panicle, score: 99.019 |
| vg0204868414 (J) | chr02 | 4868414 | T | C | 86.20% | 0.00% | T -> C |
mr1006 (All); LR P-value: 6.04E-06;
mr1052 (All); LR P-value: 4.28E-06; mr1073 (All); LR P-value: 4.21E-06; mr1207 (All); LR P-value: 2.02E-07; mr1209 (All); LR P-value: 1.32E-06; mr1303 (All); LR P-value: 4.34E-06; mr1424 (All); LR P-value: 2.43E-06; mr1507 (All); LR P-value: 8.46E-06; mr1564 (All); LR P-value: 2.88E-06; mr1596 (All); LR P-value: 4.61E-06; mr1774 (All); LR P-value: 2.03E-06; mr1787 (All); LR P-value: 8.46E-08; mr1791 (All); LR P-value: 1.20E-06; mr1808 (All); LR P-value: 4.41E-06; mr1884 (All); LR P-value: 2.69E-06; mr1939 (All); LR P-value: 7.27E-10; mr1985 (All); LR P-value: 2.94E-06; mr1158_2 (All); LR P-value: 3.40E-07 |
LOC_Os02g09480.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 92.324; most accessible tissue: Minghui63 panicle, score: 98.987 |
| vg0204868445 (J) | chr02 | 4868445 | C | T | 99.30% | 0.00% | C -> T | NA |
LOC_Os02g09480.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 95.163; most accessible tissue: Minghui63 panicle, score: 98.861 |
| vg0204868450 (J) | chr02 | 4868450 | C | T | 79.80% | 0.00% | C -> T | NA |
LOC_Os02g09480.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.140; most accessible tissue: Minghui63 panicle, score: 98.846 |
| vg0204868656 (J) | chr02 | 4868656 | A | AAAT | 94.70% | 0.70% | A -> AAAT | NA |
LOC_Os02g09480.1 Alt: AAAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: AAAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 92.937; most accessible tissue: Minghui63 panicle, score: 98.021 |
| vg0204868658 (J) | chr02 | 4868658 | A | AT | 96.10% | 0.51% | A -> AT | NA |
LOC_Os02g09480.1 Alt: AT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 92.953; most accessible tissue: Minghui63 panicle, score: 98.038 |
| vg0204868659 (J) | chr02 | 4868659 | TA | TAA | 83.60% | 0.00% | TA -> TAA,T,TAAA | NA |
LOC_Os02g09480.1 Alt: TAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: TAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09480.1 Alt: TAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09490.1 Alt: TAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.960; most accessible tissue: Minghui63 panicle, score: 98.021 |
| vg0204868662 (J) | chr02 | 4868662 | A | T | 64.90% | 0.00% | A -> T,AAT |
LOC_Os02g09480.1 Alt: AAT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: AAT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.984; most accessible tissue: Minghui63 panicle, score: 98.004 |
|
| vg0204868820 (J) | chr02 | 4868820 | G | A | 98.30% | 0.00% | G -> A | NA |
LOC_Os02g09480.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.933; most accessible tissue: Minghui63 young leaf, score: 98.617 |
| vg0204868838 (J) | chr02 | 4868838 | TA | T | 52.60% | 0.00% | TA -> TAA,T,TAAA | NA |
LOC_Os02g09480.1 Alt: TAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: TAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09480.1 Alt: TAAA| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os02g09490.1 Alt: TAAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os02g09480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.627; most accessible tissue: Minghui63 young leaf, score: 98.586 |
| vg0204868849 (J) | chr02 | 4868849 | T | G | 99.90% | 0.00% | T -> G | NA |
LOC_Os02g09480.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g09490.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.614; most accessible tissue: Minghui63 young leaf, score: 98.567 |
| vg0204868897 (J) | chr02 | 4868897 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os02g09480.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os02g09490.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 96.935; most accessible tissue: Minghui63 young leaf, score: 98.816 |
| vg0204868913 (J) | chr02 | 4868913 | C | T | 95.70% | 0.21% | C -> T | NA |
LOC_Os02g09480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 96.829; most accessible tissue: Minghui63 young leaf, score: 98.777 |
| vg0204868971 (J) | chr02 | 4868971 | T | G | 79.80% | 0.00% | T -> G | NA |
LOC_Os02g09480.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.292; most accessible tissue: Minghui63 young leaf, score: 98.806 |
| vg0204868972 (J) | chr02 | 4868972 | T | C | 91.20% | 0.00% | T -> C | NA |
LOC_Os02g09480.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 97.276; most accessible tissue: Minghui63 young leaf, score: 98.801 |
| vg0204869035 (J) | chr02 | 4869035 | T | A | 73.40% | 0.00% | A -> T |
mr1069 (All); LR P-value: 3.53E-12;
mr1149 (All); LR P-value: 4.45E-14; mr1206 (Jap_All); LR P-value: 3.60E-07; mr1229 (Jap_All); LR P-value: 1.96E-09; mr1763 (Jap_All); LR P-value: 9.87E-06; mr1246_2 (Jap_All); LR P-value: 5.89E-06; mr1388_2 (Jap_All); LR P-value: 9.38E-06; mr1404_2 (Jap_All); LR P-value: 5.28E-07; mr1555_2 (All); LR P-value: 1.17E-07; mr1620_2 (Jap_All); LR P-value: 2.92E-06; mr1671_2 (Jap_All); LR P-value: 1.30E-06; mr1748_2 (All); LR P-value: 2.68E-07; mr1880_2 (All); LR P-value: 3.15E-07; mr1880_2 (Jap_All); LR P-value: 2.90E-07 |
LOC_Os02g09480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.956; most accessible tissue: Minghui63 young leaf, score: 98.721 |
| vg0204869046 (J) | chr02 | 4869046 | T | C | 97.10% | 0.00% | T -> C | NA |
LOC_Os02g09480.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 96.964; most accessible tissue: Minghui63 young leaf, score: 98.723 |
| vg0204869094 (J) | chr02 | 4869094 | T | C | 73.50% | 0.00% | C -> T,CATTTCAG AGCATT |
mr1069 (All); LR P-value: 8.33E-12;
mr1149 (All); LR P-value: 1.25E-13; mr1206 (Jap_All); LR P-value: 2.19E-07; mr1229 (Jap_All); LR P-value: 1.84E-09; mr1763 (Jap_All); LR P-value: 3.67E-06; mr1246_2 (Jap_All); LR P-value: 6.23E-06; mr1404_2 (Jap_All); LR P-value: 7.43E-07; mr1555_2 (All); LR P-value: 3.11E-07; mr1620_2 (Jap_All); LR P-value: 3.41E-06; mr1748_2 (All); LR P-value: 2.44E-07; mr1880_2 (All); LR P-value: 6.37E-07 |
LOC_Os02g09480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09480.1 Alt: CATTTCAGAGCATT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09490.1 Alt: CATTTCAGAGCATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.689; most accessible tissue: Minghui63 young leaf, score: 98.441 |
| vg0204869109 (J) | chr02 | 4869109 | G | T | 86.40% | 0.00% | G -> T |
mr1052 (All); LR P-value: 6.16E-06;
mr1207 (All); LR P-value: 9.74E-08; mr1564 (All); LR P-value: 8.61E-06; mr1774 (All); LR P-value: 5.54E-06; mr1787 (All); LR P-value: 1.26E-07; mr1791 (All); LR P-value: 9.49E-06; mr1808 (All); LR P-value: 8.27E-06; mr1884 (All); LR P-value: 6.76E-06; mr1939 (All); LR P-value: 1.70E-09; mr1985 (All); LR P-value: 4.71E-06; mr1158_2 (All); LR P-value: 1.03E-07 |
LOC_Os02g09480.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.673; most accessible tissue: Minghui63 young leaf, score: 98.418 |
| vg0204869240 (J) | chr02 | 4869240 | T | A | 53.20% | 0.00% | T -> A |
mr1206 (Jap_All); LR P-value: 5.31E-08;
mr1229 (All); LR P-value: 2.17E-07; mr1229 (Jap_All); LR P-value: 4.03E-10; mr1343 (Ind_All); LR P-value: 4.66E-06; mr1596 (All); LR P-value: 9.83E-06; mr1596 (Jap_All); LR P-value: 8.32E-06; mr1734 (All); LR P-value: 8.31E-06; mr1748 (All); LR P-value: 1.74E-06; mr1763 (All); LR P-value: 6.56E-09; mr1763 (Jap_All); LR P-value: 1.08E-07; mr1036_2 (Ind_All); LR P-value: 1.01E-07; mr1169_2 (Ind_All); LR P-value: 1.74E-07; mr1360_2 (Ind_All); LR P-value: 5.43E-06; mr1404_2 (Jap_All); LR P-value: 3.65E-06; mr1517_2 (Ind_All); LR P-value: 1.31E-07; mr1567_2 (All); LR P-value: 1.88E-08; mr1756_2 (Ind_All); LR P-value: 8.87E-08; mr1829_2 (Ind_All); LR P-value: 2.84E-16; mr1842_2 (Ind_All); LR P-value: 2.47E-12; mr1902_2 (Ind_All); LR P-value: 2.26E-12; mr1910_2 (All); LR P-value: 1.57E-06; mr1933_2 (Ind_All); LR P-value: 1.42E-07 |
LOC_Os02g09480.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.301; most accessible tissue: Minghui63 young leaf, score: 98.208 |
| vg0204869246 (J) | chr02 | 4869246 | GA | G | 40.50% | 0.00% | GA -> G,GAA,GAAA ,GAAAA | NA |
LOC_Os02g09480.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09480.1 Alt: GAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09490.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09480.1 Alt: GAAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09490.1 Alt: GAAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09480.1 Alt: GAAA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g09490.1 Alt: GAAA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.622; most accessible tissue: Minghui63 young leaf, score: 98.324 |
| vg0204869247 (J) | chr02 | 4869247 | A | G | 76.80% | 18.15% | A -> G | NA |
LOC_Os02g09480.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 95.617; most accessible tissue: Minghui63 young leaf, score: 98.320 |
| vg0204869327 (J) | chr02 | 4869327 | C | G | 77.10% | 0.00% | C -> G | NA |
LOC_Os02g09480.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g09490.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.328; most accessible tissue: Minghui63 young leaf, score: 98.422 |
| STR0204868839 (J) | chr02 | 4868839 | AAAAA | AAAA | 53.10% | 0.00% | AAAAA -> AAAA,AAAAA A | NA |
|