Data required for Salix

<b>Files of reference genome data used in analysis</b><br>filename: Ssuchowensis.V4.1.zipdescriptions: original data downloaded from ftp://plantgenie.org/Data/PopGenIE/Salix-suchowensis, version 4.1, the reference genome is given as "Ssuchowensis_4.fa" in FASTA format<br><b>Files of alignments and scripts used to produce ontogenetic tree in Figure 4.</b>filename: Figure4 Data.zipdescriptions: <b>Figure_4.alignments.fas</b> - file contains alignments used to construct the ontogenetic tree, fasta format; <b>Figure_4.snv_mut.txt</b> - SNV mutations used to generate the alignments; <b>Figure_4.sample_panel.list</b> - sample list to be shown in the ontogenetic tree; <b>mutation2cns.pl </b> - a custom script to generate the alignments by concatenating the SNV mutations for each sample (use reference allele for non-mutated samples), usage: "perl mutation2cns.pl --input Figure_4.snv_mut.txt -s Figure_4.sample_panel.list &gt; Figure_4.alignments.fas"; <b>MyPerl</b> - custom PERL module accompany "mutation2cns.pl", need to be placed in the same folder with script or in the default PERL library path<br><b>Regional BAM files contain mapped reads of 17 BR-m mutation sites</b>filename: BAM.zipdescriptions: The 55 regional BAM files were extracted from original BAM files to only include mapping results covering the 17 BR-M mutation sites (including 10kb flanking regions). Each file was generated using codes below (the "target-region.bed" is in the format: "chrom mut_pos-10001 mut_position+10000") samtools view BAMFILE -b -L <b>target-region.bed</b> &gt;OUTPUT samtools index BAMFILE<br><b>IGV snapshots of all 17 BR-m mutations</b>filename: IGV snapshot.zipdescriptions: Screen snapshot of 17 BR-m mutation sites (+/- 55bp) from IGV (version 2.3.90, https://software.broadinstitute.org/software/igv/), in png format. All 55 samples for each mutation are shown in a single figure, with each panel presents mapping results of one sample.<br><b>Sanger sequencing data for BR-m mutation sites' verification</b><b><br></b><b>#Monoclone</b>Sanger sequencing data of monoclonal PCR product for 8 BR-m mutations sites in ab1 type.<br><br><b>#PCR</b>Sanger sequencing data of 12 BR-m mutations sites in ab1 type.<br><b>Other related files</b><br><b>Corresponded_sample_IDs.xlsx</b> - Excel file contains the corresponded sample id used in the BAM file (a short sample ID with only cutting ID) and in the paper (a full sample ID with both branch ID and cutting ID)<br><b>BR-m_mutations.Sample_readcounts.xlsx</b> - Excel file contains the detailed readcounts (number of reads for reference [i.e., ancestral ] allele and for mutation allele) of 17 BR-m mutations across 54 samples (except one poorly sequenced root sample)<br><b>Figure S4.BR-m.PCR.pptx</b>Powerpoint version for Figure S4 in paper, preview in figshare will cause partial dislocation, so we recommend to download for watching<b>Figure S5.BR-m.PCR_clone.pptx</b><br>Powerpoint version for Figure S5 in paper, preview in figshare will cause partial dislocation, so we recommend to download for watching