title: Mutant_Extremes_R1
design: For the construction of DNA bulks, 15 Resistant and 15 Susceptible bulk leaf samples were used for QTL-seq analysis using next-gen NGS technologies. Finally, 2 DNA bulks were included in the extreme groups parallel marked PRT (A-O) for pooled resistant types and PST (1-15) for pooled susceptible types. Parent samples were kept in different tubes and marked P for TI-26 and 16 for BPT-5204. Isolated Wild-type sheath blight susceptible bulks BPT-5204 and Mutant-type TI-26 sheath blight resistant bulks from the F2 population were sequenced to a 30X genome coverage. Reads were superimposed on the respective reference genome of indica using BWA (mem). DNA samples were pooled in equimolar concentration of ~ 1 g per sample and processed by paired-end sequencing libraries with the help of Illumina TruSeq Nano Library Prep Kit, at Agrigenome labs. Next generation sequencing was performed on Illumina Hiseq 2000. FastQC program and Trimmomatic v0.38 were used to evaluate quality of raw reads. Removal of paired-end adapters sequence of raw reads was performed using the FASTX toolkit program (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Quality checks for reads were performed to obtain mean base Phred quality of >30 in the tape-station profile of the library that consisted of read lengths from 303 to 850 base pair across all four samples.