A first look at the first ZEN run

PNAs (blockers for mitochondrial and chloroplast amplification)

  • More organelles were filtered from the leaves than the roots, sediment, or water.
average % loss by sample type
Leaf 26.5518607264
Root 10.6381529905
Sediment 5.1730348426
Water 13.0591363787
  • using PNAs did not result in an overall loss of reads
# filtered reads
PNA 389011
no PNA 411059
  • in progress: do we see more chimeras with PNA use?

Run summary statistics

    • 533 samples, including kit controls and PNA tests
    • reads per sample (after filtration) ranged from 5 – 206,661
    • the kit control with the most reads had 6549
    • 306 (57.4%) of the samples had fewer than 6549 reads, we’ll call these low-abundance samples
    • breakdown of low-abundance samples by type
Leaf Water Roots Sediment
126 (41.1%) 109 (35.6%) 32 (8.8%) 33 (10.8%)
  • in progress: not sure, I published this post by accident

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