312 variations found. Os01g0113800/LOC_Os01g02360 (resistance-related receptor-like kinase; putative; expressed), ranging from 745,451 bp to 748,945 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g02360 | resistance-related receptor-like kinase, putative, expressed; RAP ID: Os01g0113800; MSU ID: LOC_Os01g02360 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| STR0100746787 (J) | chr01 | 746787 | ACAACAC AAC | ACAACAC AA | 60.60% | 0.00% | ACAACACAAC -> ACAACACAA | NA |
|
| STR0100747322 (J) | chr01 | 747322 | AAAAAAA | AAAAAA | 62.50% | 0.00% | AAAAAAA -> AAAAAA | NA |
|
| vg0100745463 (J) | chr01 | 745463 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os01g02360.1 Alt: A| 5_prime_UTR_premature_start_codon_gain_variant LOW(snpEff)
LOC_Os01g02360.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os01g02334.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g02350.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.968; most accessible tissue: Zhenshan97 root, score: 93.720 |
| vg0100745486 (J) | chr01 | 745486 | A | G | 63.90% | 3.91% | A -> G |
mr1030_2 (All); LR P-value: 1.09E-08;
mr1221_2 (Ind_All); LR P-value: 3.21E-09; mr1296_2 (All); LR P-value: 1.41E-06; mr1296_2 (Ind_All); LR P-value: 4.81E-06; mr1388_2 (All); LR P-value: 1.44E-09; mr1576_2 (All); LR P-value: 1.73E-08; mr1582_2 (All); LR P-value: 7.29E-08; mr1743_2 (All); LR P-value: 1.50E-06; mr1870_2 (Ind_All); LR P-value: 2.96E-06; mr1882_2 (All); LR P-value: 5.68E-06; mr1882_2 (Ind_All); LR P-value: 4.27E-06 |
LOC_Os01g02360.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 84.027; most accessible tissue: Zhenshan97 root, score: 93.485 |
| vg0100745507 (J) | chr01 | 745507 | A | T | 63.90% | 0.00% | A -> T |
mr1030_2 (All); LR P-value: 1.30E-08;
mr1060_2 (All); LR P-value: 9.40E-06; mr1221_2 (Ind_All); LR P-value: 9.53E-10; mr1296_2 (All); LR P-value: 1.44E-06; mr1296_2 (Ind_All); LR P-value: 4.49E-06; mr1388_2 (All); LR P-value: 1.81E-09; mr1568_2 (Ind_All); LR P-value: 6.27E-06; mr1576_2 (All); LR P-value: 6.51E-09; mr1582_2 (All); LR P-value: 7.60E-08; mr1743_2 (All); LR P-value: 1.70E-06; mr1882_2 (All); LR P-value: 8.60E-06; mr1882_2 (Ind_All); LR P-value: 8.18E-06 |
LOC_Os01g02360.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 84.256; most accessible tissue: Zhenshan97 root, score: 93.125 |
| vg0100745511 (J) | chr01 | 745511 | T | C | 63.90% | 0.00% | T -> C |
mr1030_2 (All); LR P-value: 1.30E-08;
mr1060_2 (All); LR P-value: 9.40E-06; mr1221_2 (Ind_All); LR P-value: 9.53E-10; mr1296_2 (All); LR P-value: 1.44E-06; mr1296_2 (Ind_All); LR P-value: 4.49E-06; mr1388_2 (All); LR P-value: 1.81E-09; mr1568_2 (Ind_All); LR P-value: 6.27E-06; mr1576_2 (All); LR P-value: 6.51E-09; mr1582_2 (All); LR P-value: 7.60E-08; mr1743_2 (All); LR P-value: 1.70E-06; mr1882_2 (All); LR P-value: 8.60E-06; mr1882_2 (Ind_All); LR P-value: 8.18E-06 |
LOC_Os01g02360.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.911; most accessible tissue: Zhenshan97 root, score: 93.067 |
| vg0100745517 (J) | chr01 | 745517 | T | C | 63.90% | 0.00% | T -> C |
mr1030_2 (All); LR P-value: 1.30E-08;
mr1060_2 (All); LR P-value: 9.40E-06; mr1221_2 (Ind_All); LR P-value: 9.53E-10; mr1296_2 (All); LR P-value: 1.44E-06; mr1296_2 (Ind_All); LR P-value: 4.49E-06; mr1388_2 (All); LR P-value: 1.81E-09; mr1568_2 (Ind_All); LR P-value: 6.27E-06; mr1576_2 (All); LR P-value: 6.51E-09; mr1582_2 (All); LR P-value: 7.60E-08; mr1743_2 (All); LR P-value: 1.70E-06; mr1882_2 (All); LR P-value: 8.60E-06; mr1882_2 (Ind_All); LR P-value: 8.18E-06 |
LOC_Os01g02360.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.939; most accessible tissue: Zhenshan97 root, score: 92.915 |
| vg0100745527 (J) | chr01 | 745527 | A | AGT | 92.30% | 0.57% | A -> AGT | NA |
LOC_Os01g02360.1 Alt: AGT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: AGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: AGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.639; most accessible tissue: Zhenshan97 root, score: 92.594 |
| vg0100745529 (J) | chr01 | 745529 | TACACAC ACACACA CACACAC | TACACAC ACACAC | 53.90% | 4.21% | TACACACACA CACACACACA C -> TACACACACA C,TACACACA CACAC,TACA CACACACACA CACACACACA CACACAC,TA CACACACACA CACACACACA CACAC,T,TA CACACACACA CACACACACA CACACACACA C | NA |
LOC_Os01g02360.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: TACACACACAC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: TACACACACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: TACACACACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: TACACACACACACACACACACACACACACACAC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: TACACACACACACACACACACACACACACACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: TACACACACACACACACACACACACACACACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: TACACACACACAC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: TACACACACACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: TACACACACACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: TACACACACACACACACACACACACACACAC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: TACACACACACACACACACACACACACACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: TACACACACACACACACACACACACACACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: TACACACACACACACACACACACACAC| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: TACACACACACACACACACACACACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: TACACACACACACACACACACACACAC| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.520; most accessible tissue: Zhenshan97 root, score: 92.594 |
| vg0100745530 (J) | chr01 | 745530 | A | G | 67.30% | 11.19% | A -> G | NA |
LOC_Os01g02360.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.520; most accessible tissue: Zhenshan97 root, score: 92.594 |
| vg0100745531 (J) | chr01 | 745531 | C | T | 67.20% | 11.36% | C -> T | NA |
LOC_Os01g02360.1 Alt: T| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 83.633; most accessible tissue: Zhenshan97 root, score: 92.594 |
| vg0100745533 (J) | chr01 | 745533 | CACACAC ACACACA CACACAC ACAGAGA GAG | CAG | 63.80% | 11.30% | CACACACACA CACACACACA CACAGAGAGA G -> CAG,C,CAGA G | NA |
LOC_Os01g02360.1 Alt: CAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: CAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: CAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: CAGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: CAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: CAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.418; most accessible tissue: Zhenshan97 root, score: 92.145 |
| vg0100745535 (J) | chr01 | 745535 | CACACAC ACACACA CACACAC AGAGAGA GAGAG | C | 54.20% | 13.01% | CACACACACA CACACACACA CAGAGAGAGA GAG -> C,CAGAGAGA GAG,CAGAGA GAG,GACACA CACACACACA CACACAGAGA GAGAGAG,CA G | NA |
LOC_Os01g02360.1 Alt: CAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: CAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: CAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: CAGAGAGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: CAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: CAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: CAGAGAGAGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: CAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: CAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: GACACACACACACACACACACAGAGAGAGAGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: GACACACACACACACACACACAGAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: GACACACACACACACACACACAGAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 83.525; most accessible tissue: Zhenshan97 root, score: 92.145 |
| vg0100745537 (J) | chr01 | 745537 | CACACAC ACACACA CACACAG AGAGAGA GAG | C | 41.10% | 19.93% | CACACACACA CACACACACA GAGAGAGAGA G -> C,GACACACA CACACACACA CAGAGAGAGA GAG,CAGAGA GAGAG,CAGA GAGAG | NA |
LOC_Os01g02360.1 Alt: CAGAGAGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: CAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: CAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: CAGAGAGAGAG| 5_prime_UTR_variant MODIFIER(snpEff) LOC_Os01g02334.1 Alt: CAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g02350.1 Alt: CAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: GACACACACACACACACACAGAGAGAGAGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: GACACACACACACACACACAGAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: GACACACACACACACACACAGAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.641; most accessible tissue: Zhenshan97 root, score: 91.389 |
| vg0100745539 (J) | chr01 | 745539 | C | G | 41.90% | 35.12% | C -> G | NA |
LOC_Os01g02360.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 82.570; most accessible tissue: Zhenshan97 root, score: 91.301 |
| vg0100745541 (J) | chr01 | 745541 | C | G | 92.80% | 3.07% | C -> G | NA |
LOC_Os01g02360.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 82.570; most accessible tissue: Zhenshan97 root, score: 91.301 |
| vg0100745545 (J) | chr01 | 745545 | CACACAC ACACAGA GAG | C | 62.50% | 29.83% | CACACACACA CAGAGAG -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g02360.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.927; most accessible tissue: Zhenshan97 root, score: 91.257 |
| vg0100745549 (J) | chr01 | 745549 | C | G | 60.70% | 34.62% | C -> G,CGT | NA |
LOC_Os01g02360.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: CGT| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: CGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: CGT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.859; most accessible tissue: Zhenshan97 root, score: 91.211 |
| vg0100745551 (J) | chr01 | 745551 | C | G | 94.90% | 3.03% | C -> G | NA |
LOC_Os01g02360.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 82.838; most accessible tissue: Zhenshan97 root, score: 91.211 |
| vg0100745553 (J) | chr01 | 745553 | CACAGAG AGAG | GACAGAG AGAG | 67.20% | 24.52% | CACAGAGAGA G -> CAGAGAG,GA CAGAGAGAG, C | NA |
LOC_Os01g02360.1 Alt: GACAGAGAGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g02334.1 Alt: GACAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: GACAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: CAGAGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: CAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: CAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 82.872; most accessible tissue: Zhenshan97 root, score: 91.165 |
| vg0100745555 (J) | chr01 | 745555 | CAGAGAG AGAGAGA GAG | GAGAGAG AGAGAGA GAG | 35.50% | 29.77% | CAGAGAGAGA GAGAGAG -> GAGAGAGAGA GAGAGAG,CA GAGAGAG,C, CAGAGAGAGA GAGAG,CAGA GAGAGAGAG, CACAGAGAGA GAGAGAGAGA GAGAG | NA |
LOC_Os01g02360.1 Alt: CAGAGAGAG| frameshift_variant&start_lost HIGH(snpEff)/silent_mutation(CooVar)
LOC_Os01g02360.1 Alt: CAGAGAGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: CAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: CAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: CACAGAGAGAGAGAGAGAGAGAGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: CACAGAGAGAGAGAGAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: CACAGAGAGAGAGAGAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: C| frameshift_variant&start_lost HIGH(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: CAGAGAGAGAGAGAG| frameshift_variant&start_lost HIGH(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: CAGAGAGAGAGAGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: CAGAGAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: GAGAGAGAGAGAGAGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: GAGAGAGAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: GAGAGAGAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: CAGAGAGAGAGAG| frameshift_variant&start_lost HIGH(snpEff)/silent_mutation(CooVar) LOC_Os01g02360.1 Alt: CAGAGAGAGAGAG| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: CAGAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: CAGAGAGAGAGAG| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.483; most accessible tissue: Zhenshan97 root, score: 90.979 |
| vg0100745557 (J) | chr01 | 745557 | G | C | 45.40% | 31.82% | G -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g02360.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.439; most accessible tissue: Zhenshan97 root, score: 90.931 |
| vg0100745559 (J) | chr01 | 745559 | G | C | 81.60% | 0.78% | G -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g02360.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.398; most accessible tissue: Zhenshan97 root, score: 90.931 |
| vg0100745561 (J) | chr01 | 745561 | G | C | 82.70% | 0.76% | G -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g02360.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.401; most accessible tissue: Zhenshan97 root, score: 90.835 |
| vg0100745563 (J) | chr01 | 745563 | G | C | 83.00% | 0.78% | G -> C |
mr1042 (Ind_All); LR P-value: 3.44E-06;
mr1043 (Ind_All); LR P-value: 1.60E-06; mr1050 (Ind_All); LR P-value: 1.50E-06; mr1059 (Ind_All); LR P-value: 2.85E-10; mr1110 (Ind_All); LR P-value: 1.05E-07; mr1143 (Ind_All); LR P-value: 1.75E-13; mr1167 (Ind_All); LR P-value: 3.28E-12; mr1272 (Ind_All); LR P-value: 6.74E-07; mr1333 (Ind_All); LR P-value: 5.04E-06; mr1336 (Jap_All); LMM P-value: 8.92E-06; LR P-value: 8.92E-06; mr1399 (Ind_All); LR P-value: 1.49E-06; mr1458 (Ind_All); LR P-value: 2.02E-08; mr1479 (Ind_All); LR P-value: 3.92E-07; mr1502 (Ind_All); LR P-value: 1.03E-06; mr1535 (Ind_All); LR P-value: 7.14E-12; mr1593 (Ind_All); LR P-value: 2.35E-09; mr1608 (All); LR P-value: 1.14E-08; mr1608 (Ind_All); LR P-value: 6.51E-06; mr1675 (Ind_All); LR P-value: 3.68E-12; mr1677 (Ind_All); LR P-value: 5.21E-06; mr1686 (Ind_All); LR P-value: 2.81E-06; mr1726 (Ind_All); LR P-value: 1.27E-09; mr1912 (Ind_All); LR P-value: 7.82E-06; mr1950 (Ind_All); LR P-value: 5.33E-08; mr1969 (Ind_All); LR P-value: 2.66E-12; mr1975 (Ind_All); LR P-value: 3.12E-06; mr1995 (Ind_All); LR P-value: 4.55E-15; mr1024_2 (Ind_All); LR P-value: 3.36E-06; mr1110_2 (Ind_All); LR P-value: 1.97E-07; mr1113_2 (Ind_All); LR P-value: 4.34E-06; mr1167_2 (Ind_All); LR P-value: 4.44E-08; mr1195_2 (Ind_All); LR P-value: 5.45E-10; mr1221_2 (Ind_All); LR P-value: 1.56E-08; mr1360_2 (All); LR P-value: 3.86E-07; mr1360_2 (Ind_All); LR P-value: 1.07E-06; mr1378_2 (Ind_All); LR P-value: 6.03E-08; mr1383_2 (Ind_All); LR P-value: 4.77E-08; mr1458_2 (Ind_All); LR P-value: 2.24E-08; mr1593_2 (Ind_All); LR P-value: 6.93E-10; mr1739_2 (All); LR P-value: 1.83E-09; mr1739_2 (Ind_All); LR P-value: 1.84E-09; mr1794_2 (Ind_All); LR P-value: 1.91E-11; mr1895_2 (Ind_All); LR P-value: 3.50E-06 |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g02360.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02334.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g02350.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 82.700; most accessible tissue: Zhenshan97 root, score: 91.026 |
Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China
Comments or Questions? Please contact us. Our website: http://xielab.ncpgr.cn/