# Sample files — credits & licenses

Bundled sample files used by each tool's "Open sample" picker: .ab1 chromatograms (ab1lens) and
.gb GenBank records (gbatlas).

## u6-grna-1.ab1

- Construct: 2×U6-driven gRNA (CRISPR) construct, Sanger trace (ABI 3730), 987 bp.
- Source: sangerseq_viewer — `example_data/ab1/Spec-2xU6gRNA-1.ab1`
  https://github.com/ponnhide/sangerseq_viewer
- License: MIT — Copyright (c) 2022 Yachielab

  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
  in the Software without restriction, including without limitation the rights
  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  copies of the Software, and to permit persons to whom the Software is
  furnished to do so, subject to the following conditions:

  The above copyright notice and this permission notice shall be included in all
  copies or substantial portions of the Software.

  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  SOFTWARE.

## u6-grna-2.ab1

- Construct: same 2×U6 gRNA family as u6-grna-1.ab1 — a sibling Sanger read (ABI 3730),
  1041 bp. Pairs with u6-grna-1.ab1 for the two-files diff.
- Source: sangerseq_viewer — `example_data/ab1/Spec-2xU6gRNA-2.ab1`
  https://github.com/ponnhide/sangerseq_viewer
- License: MIT — Copyright (c) 2022 Yachielab (full text above).

## hand-edited-sanger.ab1

- A Sanger read (ABI 3500, sample "HV1_F", run 2021-03-25) that carries two basecall
  versions — the software calls (PBAS2, 413 bp) and a hand-edited version (PBAS1, 376 bp) — used to
  demo the Called/Edited toggle and the edits navigator. Also the `edited-differs-from-called.ab1`
  fixture used by the tests.
- Source: fishka.bio's own data.
- License: MIT — Copyright (c) 2026 fishka.bio (full text above).

## phix174-phage.gb

- Escherichia phage φX174, complete genome — 5,386 bp, circular ssDNA. The first genome ever fully
  sequenced (Sanger et al., 1977); its overlapping genes and origin-spanning join feature make it a
  good stress test for the Scene view.
- Source: NCBI GenBank, accession NC_001422.1
  https://www.ncbi.nlm.nih.gov/nuccore/NC_001422.1
- License: none — GenBank sequence/annotation records are public domain data (no copyright
  restriction on the database content itself).

## murine-sarcoma-virus.gb

- Murine sarcoma virus, complete genome — 5,833 bp, linear ssRNA (retrovirus). Carries a joined
  (ribosomal-frameshift) CDS.
- Source: NCBI GenBank, accession NC_001363.1
  https://www.ncbi.nlm.nih.gov/nuccore/NC_001363.1
- License: none — GenBank sequence/annotation records are public domain data.

## lambda-phage.gb

- Enterobacteria phage lambda, complete genome — 48,502 bp, linear dsDNA, 285 annotated features.
  One of the most extensively studied genomes in molecular biology.
- Source: NCBI GenBank, accession NC_001416.1
  https://www.ncbi.nlm.nih.gov/nuccore/NC_001416.1
- License: none — GenBank sequence/annotation records are public domain data.

## readhit/plasmid-2xu6grna.gb · readhit/plasmid-2xu6grna-3.ab1

- The map of the pUC19-Spec-2×U6-gRNA construct (4,655 bp, circular) and a third Sanger trace of it.
  Used by readhit's "plasmid" sample together with `u6-grna-1.ab1` and `u6-grna-2.ab1` above: three
  reads against the construct's own map, which agree with each other to 99% and disagree with the map
  in exactly the two 20 bp gRNA spacer sites.
- Source: sangerseq_viewer — `example_data/puc19_spec_2xu6grna.gb` and
  `example_data/ab1/Spec-2xU6gRNA-3.ab1`
  https://github.com/ponnhide/sangerseq_viewer
- License: MIT — Copyright (c) 2022 Yachielab (full text under u6-grna-1.ab1 above).

## readhit/sars-spike-reference.fasta · readhit/sars-spike-illumina.fastq

- readhit's "amplicon" sample: a 451 bp window of the SARS-CoV-2 spike NTD (MN908947.3:21930–22380)
  and 400 Illumina reads over it — 200 from each mate of one ARTIC v3 amplicon. Every read carries the
  3 bp deletion at 21993–21995 (ΔY144, lineage Alpha).
- Source: reads — Zenodo record 5036687, "Training data for _Identification of allelic variants in
  SARS-CoV-2 from deep sequencing reads_" (Bérénice Batut, Wolfgang Maier), run ERR5949465 of the
  COVID-19 Genomics UK Consortium. https://zenodo.org/records/5036687
  Reference window — INSDC accession MN908947.3 (Wuhan-Hu-1).
- License: reads — Creative Commons Attribution 4.0 International (CC-BY-4.0). Reference — none;
  INSDC sequence records are public domain data.

## readhit/sars-orf7a-reference.fasta · readhit/sars-orf7a-sanger.fastq · readhit/sars-orf7a-illumina.fastq

- readhit's "mixed" sample, and the reason the tool takes both kinds of read at once: ONE specimen
  (BioSample SAMN15150526) sequenced by BOTH methods, over a 580 bp window of ORF6/ORF7a
  (MN908947.3:26981–27560). Two Sanger reads (forward SRR12366061, reverse SRR12366060) and 250
  Illumina reads (SRR11939558) of that same material — Sanger over a pileup, and the two agree.
- Source: NCBI SRA / ENA, BioProject PRJNA610428. Reads were selected by exact k-mer containment in
  the window, which is also what keeps host sequence out of a metatranscriptomic run.
  https://www.ncbi.nlm.nih.gov/bioproject/PRJNA610428
- License: none — INSDC read records are freely available data; cited by accession.

All three sets are rebuilt by `node tools/build-readhit-samples.js`, which carries the exact URLs,
windows and selection rules.
