FASTQ TO PHYLOGENY | PART 8 | DESIGN NOTES
Author: Syed Adnan Haider

This practice dataset is identical to Part 7. It is entirely synthetic.
It is NOT biological, clinical, or viral surveillance data.

Reference length: 2,400 bases
Input reads: 300 single-end 100-base reads
Generated from reference: 280 reads
Unrelated background: 20 reads
Deliberately uncovered reference positions: 1051 through 1400 (inclusive, 350 bases)

Independently reconstructed from the known synthetic read placements, assuming
all reference-derived reads map at their intended position:
  Mean read depth over 2400 positions: 11.67x
  Breadth at >=1x: 2050 / 2400 = 85.42%
  Breadth at >=10x: 1599 / 2400 = 66.625%
  Zero-depth positions: 350

THESE ARE SIMULATION-DESIGN EXPECTATIONS, NOT MEASURED SAMTOOLS OUTPUTS.
Your results should be checked with samtools; aligner and filter settings may
change mapped reads and depth. Never report this illustration as real data.
