17 variations found. LOC_Os08g33750 (myb-like DNA-binding domain containing protein; expressed), ranging from 21,089,941 bp to 21,092,108 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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0821091705 (J) | chr08 | 21091705 | TGCTGCT | T | 65.80% | 0.00% | T -> TGCTGCT | NA |
|
| vg0821089960 (J) | chr08 | 21089960 | G | T | 68.10% | 0.00% | T -> G |
mr1040 (All); LR P-value: 1.30E-08;
mr1179 (All); LR P-value: 2.81E-18; mr1362 (All); LR P-value: 1.22E-12; mr1410 (All); LMM P-value: 9.73E-07; LR P-value: 1.14E-14; mr1410 (Jap_All); LR P-value: 2.79E-14; mr1668 (Jap_All); LR P-value: 1.51E-06; mr1836 (All); LR P-value: 1.31E-08; mr1401_2 (All); LR P-value: 1.33E-22; mr1410_2 (All); LMM P-value: 5.59E-06; LR P-value: 1.73E-15; mr1410_2 (Jap_All); LR P-value: 3.67E-14; mr1746_2 (Jap_All); LR P-value: 2.72E-08; mr1885_2 (All); LR P-value: 1.32E-07; mr1940_2 (All); LR P-value: 5.89E-09 |
LOC_Os08g33750.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g33750.2 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33740.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 63.004; most accessible tissue: Callus, score: 89.685 |
| vg0821090216 (J) | chr08 | 21090216 | AT | A | 99.30% | 0.00% | AT -> A,ATT | NA |
LOC_Os08g33750.1 Alt: ATT| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g33750.2 Alt: ATT| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os08g33740.1 Alt: ATT| downstream_gene_variant MODIFIER(snpEff) LOC_Os08g33750.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os08g33750.2 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff) LOC_Os08g33740.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 77.988; most accessible tissue: Callus, score: 95.785 |
| vg0821090264 (J) | chr08 | 21090264 | CTATA | CTATATA TATATAT ATATA | 41.80% | 3.20% | CTATATATAT ATATATATA -> CTATA,CTA, CTATATA,CT ATATATATAT ATATA,C | NA |
LOC_Os08g33750.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g33750.2 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33740.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33750.1 Alt: CTA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33750.2 Alt: CTA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33740.1 Alt: CTA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33750.1 Alt: CTATATATATATATATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33750.2 Alt: CTATATATATATATATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33740.1 Alt: CTATATATATATATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33750.1 Alt: CTATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33750.2 Alt: CTATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33740.1 Alt: CTATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os08g33750.1 Alt: CTATATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33750.2 Alt: CTATATA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33740.1 Alt: CTATATA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.843; most accessible tissue: Callus, score: 95.785 |
| vg0821090310 (J) | chr08 | 21090310 | T | C | 72.30% | 0.00% | C -> T |
LOC_Os08g33750.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g33750.2 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33740.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.158; most accessible tissue: Callus, score: 95.785 |
|
| vg0821090543 (J) | chr08 | 21090543 | ATTCTTC TTCTTG | A | 99.50% | 0.00% | ATTCTTCTTC TTG -> A | NA |
LOC_Os08g33750.1 Alt: A| inframe_deletion MODERATE(snpEff)
LOC_Os08g33750.2 Alt: A| inframe_deletion MODERATE(snpEff) LOC_Os08g33740.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.829; most accessible tissue: Zhenshan97 panicle, score: 96.414 |
| vg0821090578 (J) | chr08 | 21090578 | G | T | 68.00% | 0.02% | T -> G |
mr1040 (All); LR P-value: 2.06E-07;
mr1410 (Jap_All); LR P-value: 9.85E-13; mr1228_2 (All); LR P-value: 7.97E-10; mr1401_2 (All); LR P-value: 1.22E-24; mr1410_2 (All); LR P-value: 3.12E-14; mr1410_2 (Jap_All); LR P-value: 8.52E-13; mr1885_2 (All); LR P-value: 4.12E-08; mr1924_2 (All); LR P-value: 2.40E-21; mr1940_2 (All); LR P-value: 1.06E-09 |
LOC_Os08g33750.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g33750.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os08g33750.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os08g33750.2 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.195; most accessible tissue: Zhenshan97 panicle, score: 95.951 |
| vg0821090603 (J) | chr08 | 21090603 | T | C | 72.10% | 0.19% | C -> T |
LOC_Os08g33750.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g33750.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os08g33750.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os08g33750.2 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 83.339; most accessible tissue: Zhenshan97 panicle, score: 95.855 |
|
| vg0821090742 (J) | chr08 | 21090742 | T | C | 68.00% | 0.00% | C -> T |
mr1040 (All); LR P-value: 9.94E-09;
mr1362 (All); LR P-value: 9.43E-13; mr1410 (All); LMM P-value: 2.26E-06; LR P-value: 2.56E-14; mr1410 (Jap_All); LR P-value: 2.79E-14; mr1668 (Jap_All); LR P-value: 1.51E-06; mr1836 (All); LR P-value: 9.95E-09; mr1401_2 (All); LR P-value: 6.57E-23; mr1410_2 (All); LMM P-value: 9.12E-06; LR P-value: 2.75E-15; mr1410_2 (Jap_All); LR P-value: 3.67E-14; mr1746_2 (Jap_All); LR P-value: 2.72E-08; mr1885_2 (All); LR P-value: 1.48E-07; mr1940_2 (All); LR P-value: 3.07E-09 |
LOC_Os08g33750.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g33750.2 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 85.182; most accessible tissue: Zhenshan97 panicle, score: 93.351 |
| vg0821090804 (J) | chr08 | 21090804 | T | C | 68.10% | 0.00% | C -> T |
mr1040 (All); LR P-value: 1.34E-08;
mr1179 (All); LR P-value: 8.17E-19; mr1213 (Jap_All); LR P-value: 5.13E-06; mr1362 (All); LR P-value: 9.60E-13; mr1410 (All); LR P-value: 1.92E-14; mr1410 (Jap_All); LR P-value: 1.51E-13; mr1668 (Jap_All); LR P-value: 3.37E-07; mr1836 (All); LR P-value: 1.16E-08; mr1980 (Jap_All); LR P-value: 9.34E-10; mr1401_2 (All); LR P-value: 3.97E-22; mr1410_2 (All); LR P-value: 3.27E-15; mr1410_2 (Jap_All); LR P-value: 2.48E-13; mr1885_2 (All); LR P-value: 8.16E-08; mr1940_2 (All); LR P-value: 3.72E-09 |
LOC_Os08g33750.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g33750.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 84.493; most accessible tissue: Zhenshan97 panicle, score: 92.270 |
| vg0821090824 (J) | chr08 | 21090824 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os08g33750.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os08g33750.2 Alt: T| missense_variant MODERATE(snpEff) LOC_Os08g33740.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.180; most accessible tissue: Zhenshan97 panicle, score: 89.846 |
| vg0821091028 (J) | chr08 | 21091028 | CT | C | 62.40% | 0.00% | C -> CT,CTTT,CT T | NA |
LOC_Os08g33740.1 Alt: CT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g33750.1 Alt: CT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33750.2 Alt: CT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33740.1 Alt: CTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33750.1 Alt: CTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33750.2 Alt: CTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33740.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33750.1 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g33750.2 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 79.394; most accessible tissue: Zhenshan97 panicle, score: 83.410 |
| vg0821091114 (J) | chr08 | 21091114 | G | C | 72.20% | 0.11% | C -> G |
mr1301 (All); LMM P-value: 5.67E-06;
mr1410 (All); LMM P-value: 3.85E-09; LR P-value: 2.18E-17; mr1410 (Jap_All); LR P-value: 7.22E-14; mr1514 (All); LR P-value: 6.88E-08; mr1563 (All); LR P-value: 4.52E-44; mr1668 (Jap_All); LR P-value: 1.78E-06; mr1980 (All); LR P-value: 3.81E-30; mr1410_2 (All); LMM P-value: 2.18E-07; LR P-value: 4.57E-16; mr1410_2 (Jap_All); LR P-value: 1.02E-13; mr1668_2 (Jap_All); LR P-value: 5.50E-06; mr1746_2 (Jap_All); LR P-value: 1.42E-08 |
LOC_Os08g33750.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g33750.2 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os08g33750.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os08g33750.2 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 75.235; most accessible tissue: Zhenshan97 panicle, score: 82.336 |
| vg0821091267 (J) | chr08 | 21091267 | C | T | 94.30% | 0.00% | C -> T,A |
LOC_Os08g33750.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g33750.2 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os08g33750.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os08g33750.2 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 81.693; most accessible tissue: Zhenshan97 panicle, score: 88.062 |
|
| vg0821091662 (J) | chr08 | 21091662 | C | A | 99.10% | 0.00% | C -> A | NA |
LOC_Os08g33750.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 83.896; most accessible tissue: Zhenshan97 panicle, score: 93.752 |
| vg0821091704 (J) | chr08 | 21091704 | GTGCTGC | G | 71.50% | 0.00% | G -> GTGCTGC,GT GC | NA |
LOC_Os08g33750.1 Alt: GTGC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os08g33750.2 Alt: GTGC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os08g33750.1 Alt: GTGCTGC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os08g33750.2 Alt: GTGCTGC| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 88.079; most accessible tissue: Zhenshan97 panicle, score: 93.936 |
| vg0821091969 (J) | chr08 | 21091969 | C | G | 99.30% | 0.00% | C -> G | NA |
LOC_Os08g33750.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g33750.2 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff) The average chromatin accessibility score: 94.095; most accessible tissue: Zhenshan97 panicle, score: 98.115 |
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