e-TILLING    for NGS-based in silico reverse genetics screening of specific accession or mutant
query (input):
Database:
cutoff settings: GATK's GQ :    read depth :    display TOP [x] accessions/mutants in each genotype (html) :   
variant report filter:
[INFO]
Currently, one dataset is available as a trial. It is based on the NGS dataset of 320 natural accessions (Zhao et al. 2019, Nature Genetics 51[11] 1607-1615).
In future, additional NGS dataset may be added (e.g. Harukei-3 EMS mutant population).




[! Below is example]


Summary | selected DB=[Illumina-based DNA variant dataset of 320 lines (published data of Zhao et al. 2019, reference=Harukei-3 ver1.41)]
Query mutant
found
variant
found
aa
changing
nonsense Arabidopsis best homologue Arabidopsis homologue function E-value score
MELO3C015737 8 2 7 - => AT3G23240.1 (ATERF1) ethylene response factor 1 1.72E-55 176
MELO3C011364 36 8 14 1 => AT1G78080.1 (RAP2.4) related to AP2 4 1.33E-85 262
MELO3C010195 16 4 8 - => AT1G16060.1 (ADAP) ARIA-interacting double AP2 domain protein 1.43E-112 331
MELO3C007241 26 4 12 2 => AT4G18450.1 Integrase-type DNA-binding superfamily protein 8.40E-47 158



mutant search result (example)

*variant with higher [GQ] may be confident (e.g. GQ > 30)
*hom-alt=[homozygous ALT], hetero=[heterozygous], hom-ref=[homozygous REF], RC=[reverse complement]


Query=[MELO3C015737] | mutant found=[8] | variant found=[2] | homologue of [AT3G23240.1 (ATERF1), ethylene response factor 1]
Plant ID DP GQ %ALT Predicted
genotype
Chr. Pos. REF
[RC]
ALT
[RC]
Transcript located at mutation type a.a. change alignment
CDS
alignment
Protein
   MS_1035 12 99 58.3 hetero chr01 28119294 G [C] A [T] MELO3C015737.jh1.t1 CDS.1 missense R176W [link] [link]
   MS_1043 10 99 40.0 hetero
   MS_1037 14 99 50.0 hetero chr01 28119513 C [G] T [A] MELO3C015737.jh1.t1 CDS.1 missense V103I [link] [link]
   MS_1035 19 99 42.1 hetero
   MS_1064 11 99 36.4 hetero
   MS_1043 12 64 25.0 hetero
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Query=[MELO3C011364] | mutant found=[36] | variant found=[8] | homologue of [AT1G78080.1 (RAP2.4), related to AP2 4]
Plant ID DP GQ %ALT Predicted
genotype
Chr. Pos. REF
[RC]
ALT
[RC]
Transcript located at mutation type a.a. change alignment
CDS
alignment
Protein
   MS_1054 11 99 36.4 hetero chr03 25111088 C T MELO3C011364.jh1.t1 CDS.1 nonsense Q117* [link] [link]
   MS_1030 12 96 25.0 hetero chr03 25111091 A C MELO3C011364.jh1.t1 CDS.1 missense I118L [link] [link]
   MS_1033 11 99 54.5 hetero chr03 25111101 T C MELO3C011364.jh1.t1 CDS.1 missense V121A [link] [link]
   MS_1032 13 99 46.2 hetero
   MS_1031 11 99 36.4 hetero
   MS_1076 13 39 100.0 hom-alt chr03 25111128 T A MELO3C011364.jh1.t1 CDS.1 missense V130E [link] [link]
   MS_850 13 39 100.0 hom-alt
   MS_330 12 36 100.0 hom-alt
   MS_471 12 36 100.0 hom-alt
   MS_546 11 33 100.0 hom-alt
other [1] hom-alt...
   MS_1071 11 99 63.6 hetero
   MS_1066 10 99 50.0 hetero
   MS_1060 12 99 58.3 hetero chr03 25111554 C T MELO3C011364.jh1.t1 CDS.1 missense T272I [link] [link]
   MS_1025 16 48 100.0 hom-alt chr03 25111578 C T MELO3C011364.jh1.t1 CDS.1 missense P280L [link] [link]
   MS_1061 14 42 100.0 hom-alt
   MS_270 14 42 100.0 hom-alt
   MS_965 14 42 100.0 hom-alt
   MS_169 13 39 100.0 hom-alt
other [14] hom-alt...
   MS_1035 22 99 72.7 hetero
   MS_1038 19 99 63.2 hetero
   MS_1024 14 99 50.0 hetero
   MS_1081 13 99 38.5 hetero
   MS_919 12 99 33.3 hetero
other [3] hetero...
   MS_1032 11 57 81.8 hetero chr03 25111596 A G MELO3C011364.jh1.t1 CDS.1 missense D286G [link] [link]
   MS_1032 14 99 64.3 hetero chr03 25111657 G T MELO3C011364.jh1.t1 CDS.1 missense E306D [link] [link]
   MS_1033 11 99 54.5 hetero
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Query=[MELO3C010195] | mutant found=[16] | variant found=[4] | homologue of [AT1G16060.1 (ADAP), ARIA-interacting double AP2 domain protein]
Plant ID DP GQ %ALT Predicted
genotype
Chr. Pos. REF
[RC]
ALT
[RC]
Transcript located at mutation type a.a. change alignment
CDS
alignment
Protein
   MS_1056 15 99 46.7 hetero chr02 13198446 C [G] A [T] MELO3C010195.jh1.t1 CDS.7 missense A302S [link] [link]
   MS_1078 10 96 30.0 hetero
   MS_1031 11 57 81.8 hetero
   MS_1080 13 51 84.6 hetero
   MS_1082 10 99 50.0 hetero chr02 13198538 G [C] T [A] MELO3C010195.jh1.t1 CDS.7 missense S271Y [link] [link]
   MS_1082 10 99 50.0 hetero chr02 13198539 A [T] T [A] MELO3C010195.jh1.t1 CDS.7 missense S271T [link] [link]
   MS_1036 14 42 100.0 hom-alt chr02 13201511 T TATTAAGATGTCCGGAATGTA MELO3C010195.jh1.t1 intron.2 intron | within 2 bp from splicing junction (may affect) - - -
   MS_1080 14 99 71.4 hetero
   MS_1053 14 99 50.0 hetero
   MS_1029 14 99 35.7 hetero
   MS_1039 10 99 30.0 hetero
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Query=[MELO3C007241] | mutant found=[26] | variant found=[4] | homologue of [AT4G18450.1, Integrase-type DNA-binding superfamily protein]
Plant ID DP GQ %ALT Predicted
genotype
Chr. Pos. REF
[RC]
ALT
[RC]
Transcript located at mutation type a.a. change alignment
CDS
alignment
Protein
   MS_1049 15 45 100.0 hom-alt chr08 1657354 A C MELO3C007241.jh1.t1 CDS.1 missense Q7P [link] [link]
   MS_1042 11 33 100.0 hom-alt
   MS_1040 10 30 100.0 hom-alt
   MS_1041 10 30 100.0 hom-alt
   MS_748 11 99 45.5 hetero
   MS_1060 24 99 41.7 hetero
   MS_1043 14 99 28.6 hetero
   MS_1035 24 99 25.0 hetero
   MS_1029 10 94 30.0 hetero
other [1] hetero...
   MS_1048 10 30 100.0 hom-alt chr08 1657485 A G MELO3C007241.jh1.t1 CDS.1 missense N51D [link] [link]
   MS_1029 12 99 25.0 hetero
   MS_1035 20 75 85.0 hetero
   MS_1048 10 30 100.0 hom-alt chr08 1657497 G A MELO3C007241.jh1.t1 CDS.1 missense E55K [link] [link]
   MS_1062 11 86 27.3 hetero
   MS_1035 16 80 81.2 hetero
   MS_1030 18 44 94.4 hom-alt chr08 1657935 A G MELO3C007241.jh1.t1 CDS.1 missense M201V [link] [link]
   MS_919 12 36 100.0 hom-alt
   MS_1043 10 99 40.0 hetero
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