37 variations found. LOC_Os04g17380 (retrotransposon protein; putative; Ty3-gypsy subclass), ranging from 9,515,086 bp to 9,515,605 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515128 (J) | chr04 | 9515128 | A | G | 91.10% | 8.00% | A -> G | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 37.548; most accessible tissue: Minghui63 young leaf, score: 63.571 |
| vg0409515146 (J) | chr04 | 9515146 | A | G | 90.80% | 8.89% | A -> G | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 36.962; most accessible tissue: Minghui63 young leaf, score: 61.887 |
| vg0409515151 (J) | chr04 | 9515151 | TA | AA | 63.10% | 9.39% | TA -> AA,T |
mr1062 (Ind_All); LR P-value: 1.57E-06;
mr1403 (Ind_All); LR P-value: 1.49E-06; mr1414 (Ind_All); LR P-value: 8.91E-07; mr1830 (Ind_All); LR P-value: 8.08E-08; mr1846 (All); LMM P-value: 7.97E-06; LR P-value: 1.10E-16; mr1846 (Ind_All); LR P-value: 8.89E-13; mr1317_2 (Ind_All); LR P-value: 5.04E-07; mr1608_2 (All); LR P-value: 7.38E-07; mr1608_2 (Ind_All); LR P-value: 8.70E-07; mr1818_2 (Ind_All); LR P-value: 3.31E-07; mr1830_2 (All); LR P-value: 3.33E-12; mr1830_2 (Ind_All); LR P-value: 4.55E-10; mr1846_2 (All); LR P-value: 6.65E-25; mr1846_2 (Ind_All); LR P-value: 8.39E-22 |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: AA| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os04g17380.1 Alt: T| frameshift_variant HIGH(snpEff) LOC_Os04g17370.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g17390.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 35.779; most accessible tissue: Minghui63 young leaf, score: 61.007 |
| vg0409515156 (J) | chr04 | 9515156 | C | T | 90.80% | 8.82% | C -> T | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 35.631; most accessible tissue: Minghui63 young leaf, score: 61.887 |
| vg0409515160 (J) | chr04 | 9515160 | C | A | 90.90% | 8.80% | C -> A | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 35.228; most accessible tissue: Minghui63 young leaf, score: 61.887 |
| vg0409515192 (J) | chr04 | 9515192 | A | T | 90.80% | 8.87% | A -> T | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 35.215; most accessible tissue: Minghui63 young leaf, score: 56.213 |
| vg0409515201 (J) | chr04 | 9515201 | A | C | 77.70% | 8.95% | A -> C,ATGTCACA CCC | NA |
LOC_Os04g17380.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os04g17380.1 Alt: ATGTCACACCC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 35.860; most accessible tissue: Minghui63 young leaf, score: 56.213 |
| vg0409515202 (J) | chr04 | 9515202 | T | TGTCACA CCCTTAT TTTCG | 90.20% | 8.87% | T -> TGTCACACCC ,TGTCACACC CTTATTTTCG ,TGTCACACC CTTATTTTTG | NA |
LOC_Os04g17380.1 Alt: TGTCACACCC| stop_gained&inframe_insertion HIGH(snpEff)/inframe_variant(CooVar)
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os04g17380.1 Alt: TGTCACACCCTTATTTTTG| stop_gained&inframe_insertion HIGH(snpEff)/inframe_variant(CooVar) LOC_Os04g17380.1 Alt: TGTCACACCCTTATTTTCG| stop_gained&inframe_insertion HIGH(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 35.860; most accessible tissue: Minghui63 young leaf, score: 56.213 |
| vg0409515203 (J) | chr04 | 9515203 | T | G | 90.60% | 8.87% | T -> G | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 35.860; most accessible tissue: Minghui63 young leaf, score: 56.213 |
| vg0409515204 (J) | chr04 | 9515204 | A | ATTT | 90.20% | 8.87% | A -> ATTT,T | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: ATTT| stop_gained&disruptive_inframe_insertion HIGH(snpEff)/inframe_variant(CooVar) LOC_Os04g17380.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar) The average chromatin accessibility score: 35.917; most accessible tissue: Minghui63 young leaf, score: 56.213 |
| vg0409515205 (J) | chr04 | 9515205 | T | G | 90.00% | 8.80% | T -> C,G | NA |
LOC_Os04g17380.1 Alt: C| missense_variant MODERATE(snpEff)/stop_gained(CooVar)
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os04g17380.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 35.917; most accessible tissue: Minghui63 young leaf, score: 56.213 |
| vg0409515206 (J) | chr04 | 9515206 | A | C | 90.40% | 8.80% | A -> C,T | NA |
LOC_Os04g17380.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os04g17380.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 36.070; most accessible tissue: Minghui63 young leaf, score: 56.213 |
| vg0409515243 (J) | chr04 | 9515243 | G | A | 82.30% | 8.42% | G -> A | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 32.060; most accessible tissue: Minghui63 young leaf, score: 50.756 |
| vg0409515246 (J) | chr04 | 9515246 | G | A | 91.30% | 8.38% | G -> A | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 31.989; most accessible tissue: Minghui63 young leaf, score: 50.756 |
| vg0409515250 (J) | chr04 | 9515250 | T | Unkown | 91.40% | 8.40% | T -> A | NA |
LOC_Os04g17380.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os04g17370.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g17390.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g17400.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 31.518; most accessible tissue: Minghui63 young leaf, score: 50.756 |
| vg0409515258 (J) | chr04 | 9515258 | C | T | 90.90% | 8.38% | C -> T | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 31.545; most accessible tissue: Minghui63 young leaf, score: 50.756 |
| vg0409515260 (J) | chr04 | 9515260 | G | A | 91.40% | 8.38% | G -> A | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 31.545; most accessible tissue: Minghui63 young leaf, score: 50.756 |
| vg0409515262 (J) | chr04 | 9515262 | G | A | 91.40% | 8.40% | G -> A | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 31.463; most accessible tissue: Minghui63 young leaf, score: 50.756 |
| vg0409515266 (J) | chr04 | 9515266 | C | T | 83.80% | 8.40% | C -> T | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 31.343; most accessible tissue: Minghui63 young leaf, score: 49.581 |
| vg0409515286 (J) | chr04 | 9515286 | C | A | 84.20% | 8.40% | C -> A | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 29.234; most accessible tissue: Minghui63 young leaf, score: 43.347 |
| vg0409515288 (J) | chr04 | 9515288 | T | A | 91.00% | 8.38% | T -> A | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 29.115; most accessible tissue: Minghui63 young leaf, score: 42.042 |
| vg0409515292 (J) | chr04 | 9515292 | A | T | 91.40% | 8.40% | A -> T | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 28.722; most accessible tissue: Minghui63 young leaf, score: 40.718 |
| vg0409515303 (J) | chr04 | 9515303 | C | T | 90.80% | 8.40% | C -> T | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 26.405; most accessible tissue: Minghui63 panicle, score: 38.588 |
| vg0409515304 (J) | chr04 | 9515304 | G | Unkown | 91.40% | 8.42% | G -> GA | NA |
LOC_Os04g17380.1 Alt: GA| frameshift_variant HIGH(snpEff)
LOC_Os04g17370.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g17390.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 26.405; most accessible tissue: Minghui63 panicle, score: 38.588 |
| vg0409515310 (J) | chr04 | 9515310 | T | A | 91.40% | 8.42% | T -> A | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 25.538; most accessible tissue: Minghui63 panicle, score: 34.226 |
| vg0409515311 (J) | chr04 | 9515311 | C | T | 91.40% | 8.42% | C -> T | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 25.538; most accessible tissue: Minghui63 panicle, score: 34.226 |
| vg0409515312 (J) | chr04 | 9515312 | C | T | 91.00% | 8.44% | C -> T | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 25.538; most accessible tissue: Minghui63 panicle, score: 34.226 |
| vg0409515338 (J) | chr04 | 9515338 | G | A | 89.20% | 8.80% | G -> A | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 23.632; most accessible tissue: Minghui63 panicle, score: 34.226 |
| vg0409515347 (J) | chr04 | 9515347 | C | T | 90.80% | 8.55% | C -> T | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 23.576; most accessible tissue: Minghui63 panicle, score: 34.226 |
| vg0409515361 (J) | chr04 | 9515361 | T | C | 65.30% | 10.28% | C -> T |
mr1040 (All); LR P-value: 1.73E-07;
mr1045 (All); LR P-value: 1.74E-08; mr1072 (All); LR P-value: 1.97E-26; mr1077 (All); LR P-value: 3.01E-19; mr1156 (All); LR P-value: 9.36E-15; mr1175 (All); LR P-value: 6.34E-10; mr1206 (Jap_All); LR P-value: 3.47E-07; mr1229 (Jap_All); LR P-value: 2.44E-07; mr1241 (All); LR P-value: 3.18E-52; mr1252 (All); LR P-value: 1.53E-06; mr1277 (All); LR P-value: 1.24E-09; mr1301 (Jap_All); LR P-value: 2.13E-15; mr1378 (All); LR P-value: 4.00E-06; mr1403 (Jap_All); LR P-value: 3.49E-07; mr1663 (All); LR P-value: 2.41E-09; mr1739 (Jap_All); LR P-value: 1.18E-06; mr1741 (All); LR P-value: 2.68E-12; mr1746 (All); LR P-value: 1.15E-09; mr1785 (All); LR P-value: 5.79E-07; mr1789 (All); LR P-value: 9.08E-32; mr1844 (All); LR P-value: 3.29E-13; mr1977 (All); LR P-value: 3.65E-06; mr1982 (All); LR P-value: 6.45E-14; mr1993 (Jap_All); LR P-value: 4.87E-08; mr1248_2 (All); LR P-value: 1.28E-12; mr1301_2 (Jap_All); LR P-value: 9.04E-19; mr1410_2 (Jap_All); LR P-value: 4.51E-12; mr1520_2 (All); LR P-value: 2.49E-11; mr1993_2 (Jap_All); LR P-value: 1.90E-12 |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 23.431; most accessible tissue: Minghui63 panicle, score: 34.226 |
| vg0409515409 (J) | chr04 | 9515409 | A | C | 64.50% | 7.68% | C -> A,G |
mr1040 (All); LR P-value: 7.90E-07;
mr1045 (All); LR P-value: 5.61E-08; mr1206 (Jap_All); LR P-value: 9.55E-08; mr1229 (Jap_All); LR P-value: 4.17E-08; mr1403 (Jap_All); LR P-value: 1.66E-07; mr1663 (All); LR P-value: 1.86E-09; mr1668 (Jap_All); LR P-value: 7.59E-07; mr1739 (Jap_All); LR P-value: 7.67E-07; mr1746 (All); LR P-value: 4.20E-09; mr1785 (All); LR P-value: 5.80E-07; mr1982 (All); LR P-value: 1.37E-13; mr1301_2 (Jap_All); LR P-value: 1.64E-15; mr1991_2 (All); LR P-value: 1.14E-50; mr1991_2 (Jap_All); LR P-value: 1.97E-07 |
LOC_Os04g17380.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os04g17380.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 18.984; most accessible tissue: Minghui63 panicle, score: 25.313 |
| vg0409515411 (J) | chr04 | 9515411 | A | C | 64.50% | 7.70% | C -> A |
mr1040 (All); LR P-value: 7.90E-07;
mr1045 (All); LR P-value: 5.61E-08; mr1206 (Jap_All); LR P-value: 9.55E-08; mr1229 (Jap_All); LR P-value: 4.17E-08; mr1403 (Jap_All); LR P-value: 1.66E-07; mr1663 (All); LR P-value: 1.86E-09; mr1668 (Jap_All); LR P-value: 7.59E-07; mr1739 (Jap_All); LR P-value: 7.67E-07; mr1746 (All); LR P-value: 4.20E-09; mr1785 (All); LR P-value: 5.80E-07; mr1982 (All); LR P-value: 1.37E-13; mr1301_2 (Jap_All); LR P-value: 1.64E-15; mr1991_2 (All); LR P-value: 1.14E-50; mr1991_2 (Jap_All); LR P-value: 1.97E-07 |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 19.291; most accessible tissue: Minghui63 panicle, score: 25.313 |
| vg0409515435 (J) | chr04 | 9515435 | T | C | 89.40% | 7.60% | T -> C | NA |
LOC_Os04g17380.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.307; most accessible tissue: Callus, score: 28.075 |
| vg0409515452 (J) | chr04 | 9515452 | C | A | 85.30% | 7.36% | C -> A,T,G | NA |
LOC_Os04g17380.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os04g17380.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) LOC_Os04g17380.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 21.300; most accessible tissue: Callus, score: 28.075 |
| vg0409515514 (J) | chr04 | 9515514 | C | T | 90.30% | 8.93% | C -> T | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 23.481; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 |
| vg0409515519 (J) | chr04 | 9515519 | AACAAGC TTATAAG GAGGAAC TTGAATA TTGATCC ATG | A | 90.20% | 8.93% | AACAAGCTTA TAAGGAGGAA CTTGAATATT GATCCATG -> A | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 23.540; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 |
| vg0409515543 (J) | chr04 | 9515543 | A | AAT | 65.40% | 10.28% | AAT -> A | NA |
LOC_Os04g17380.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g17380.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 24.010; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 |