25 variations found. LOC_Os01g49570 (retrotransposon protein; putative; unclassified; expressed), ranging from 28,509,255 bp to 28,509,573 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509318 (J) | chr01 | 28509318 | C | G | 27.20% | 60.73% | C -> G,T | NA |
LOC_Os01g49570.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 20.672; most accessible tissue: Zhenshan97 panicle, score: 28.447 |
| vg0128509352 (J) | chr01 | 28509352 | G | A | 29.60% | 62.25% | G -> A | NA |
LOC_Os01g49570.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.620; most accessible tissue: Zhenshan97 panicle, score: 36.038 |
| vg0128509357 (J) | chr01 | 28509357 | C | T | 30.60% | 53.77% | C -> T | NA |
LOC_Os01g49570.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.886; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0128509373 (J) | chr01 | 28509373 | ATATAT | AGAGATG GTATAT | 25.20% | 70.17% | ATATAT -> AGAGATGGTA TAT,A | NA |
LOC_Os01g49570.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os01g49570.1 Alt: AGAGATGGTATAT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0128509374 (J) | chr01 | 28509374 | T | G | 36.80% | 53.83% | T -> G | NA |
LOC_Os01g49570.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0128509375 (J) | chr01 | 28509375 | A | AGATGG | 37.50% | 53.20% | A -> AGATGG | NA |
LOC_Os01g49570.1 Alt: AGATGG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0128509376 (J) | chr01 | 28509376 | T | G | 38.60% | 52.41% | T -> G,TCAGAGC, TC | NA |
LOC_Os01g49570.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: TC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os01g49570.1 Alt: TCAGAGC| stop_gained&disruptive_inframe_insertion HIGH(snpEff)/inframe_variant(CooVar) LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.498; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0128509378 (J) | chr01 | 28509378 | T | TCA | 25.30% | 70.31% | T -> TCA,G,TA | NA |
LOC_Os01g49570.1 Alt: TCA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g49570.1 Alt: TA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os01g49570.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.355; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0128509380 (J) | chr01 | 28509380 | AAC | A | 40.80% | 49.83% | AAC -> A | NA |
LOC_Os01g49570.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.355; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0128509381 (J) | chr01 | 28509381 | A | G | 39.90% | 51.33% | A -> G,T | NA |
LOC_Os01g49570.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.355; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0128509385 (J) | chr01 | 28509385 | T | C | 25.00% | 65.38% | T -> C | NA |
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g49570.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 21.355; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0128509396 (J) | chr01 | 28509396 | T | C | 25.10% | 63.35% | T -> C | NA |
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g49570.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 21.721; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0128509406 (J) | chr01 | 28509406 | G | T | 49.60% | 43.27% | G -> T | NA |
LOC_Os01g49570.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 21.721; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0128509408 (J) | chr01 | 28509408 | T | C | 25.20% | 57.96% | T -> C | NA |
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g49570.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 21.776; most accessible tissue: Zhenshan97 panicle, score: 39.652 |
| vg0128509427 (J) | chr01 | 28509427 | C | T | 48.50% | 44.79% | C -> T | NA |
LOC_Os01g49570.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 24.383; most accessible tissue: Callus, score: 48.491 |
| vg0128509430 (J) | chr01 | 28509430 | C | T | 25.10% | 55.31% | C -> T | NA |
LOC_Os01g49570.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 24.383; most accessible tissue: Callus, score: 48.491 |
| vg0128509434 (J) | chr01 | 28509434 | G | A | 57.90% | 30.11% | G -> A | NA |
LOC_Os01g49570.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 24.383; most accessible tissue: Callus, score: 48.491 |
| vg0128509437 (J) | chr01 | 28509437 | T | C | 25.10% | 55.46% | T -> C | NA |
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g49570.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 24.383; most accessible tissue: Callus, score: 48.491 |
| vg0128509467 (J) | chr01 | 28509467 | C | T | 24.90% | 52.01% | C -> T |
mr1047 (Jap_All); LR P-value: 3.19E-06;
mr1125 (Jap_All); LR P-value: 9.42E-06; mr1425 (Jap_All); LR P-value: 6.30E-06; mr1471 (Jap_All); LR P-value: 6.58E-07; mr1530 (Jap_All); LR P-value: 7.03E-06; mr1543 (Jap_All); LR P-value: 5.73E-07; mr1642 (Jap_All); LR P-value: 1.06E-06; mr1742 (Jap_All); LR P-value: 4.06E-07; mr1871 (Jap_All); LR P-value: 2.20E-06; mr1903 (Jap_All); LR P-value: 7.99E-07; mr1217_2 (All); LR P-value: 6.02E-13; mr1471_2 (Jap_All); LR P-value: 1.37E-11; mr1526_2 (Jap_All); LR P-value: 1.12E-08; mr1642_2 (Jap_All); LR P-value: 3.12E-10; mr1667_2 (All); LR P-value: 7.06E-11; mr1807_2 (Jap_All); LR P-value: 4.99E-07; mr1991_2 (All); LR P-value: 1.55E-52 |
LOC_Os01g49570.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 29.645; most accessible tissue: Zhenshan97 panicle, score: 49.416 |
| vg0128509483 (J) | chr01 | 28509483 | A | G | 25.00% | 52.37% | A -> G |
mr1047 (Jap_All); LR P-value: 9.77E-06;
mr1543 (Jap_All); LR P-value: 4.86E-07; mr1642 (Jap_All); LR P-value: 3.12E-06; mr1742 (Jap_All); LR P-value: 7.51E-07; mr1871 (Jap_All); LR P-value: 6.02E-06; mr1903 (Jap_All); LR P-value: 1.89E-06; mr1990 (Jap_All); LR P-value: 8.87E-06; mr1526_2 (Jap_All); LR P-value: 5.51E-08; mr1991_2 (All); LR P-value: 4.66E-51 |
LOC_Os01g49570.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 30.621; most accessible tissue: Zhenshan97 panicle, score: 49.416 |
| vg0128509492 (J) | chr01 | 28509492 | G | A | 25.00% | 52.12% | G -> A |
mr1047 (Jap_All); LR P-value: 9.77E-06;
mr1543 (Jap_All); LR P-value: 4.86E-07; mr1642 (Jap_All); LR P-value: 3.12E-06; mr1742 (Jap_All); LR P-value: 7.51E-07; mr1871 (Jap_All); LR P-value: 6.02E-06; mr1903 (Jap_All); LR P-value: 1.89E-06; mr1990 (Jap_All); LR P-value: 8.87E-06; mr1526_2 (Jap_All); LR P-value: 5.51E-08 |
LOC_Os01g49570.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 31.266; most accessible tissue: Zhenshan97 panicle, score: 49.416 |
| vg0128509535 (J) | chr01 | 28509535 | T | C | 24.90% | 53.26% | T -> C | NA |
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g49570.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 32.218; most accessible tissue: Zhenshan97 panicle, score: 49.416 |
| vg0128509559 (J) | chr01 | 28509559 | A | G | 25.00% | 56.12% | A -> G | NA |
LOC_Os01g49570.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: G| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar) LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 37.821; most accessible tissue: Zhenshan97 panicle, score: 59.590 |
| vg0128509560 (J) | chr01 | 28509560 | C | T | 29.30% | 52.01% | C -> T | NA |
LOC_Os01g49570.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 37.821; most accessible tissue: Zhenshan97 panicle, score: 59.590 |
| vg0128509569 (J) | chr01 | 28509569 | A | G | 25.00% | 56.83% | A -> G | NA |
LOC_Os01g49570.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g49570.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 38.604; most accessible tissue: Zhenshan97 panicle, score: 59.590 |