BED6 Intervals — 0-Based Half-Open Coordinates (.bed)
The same six features as the GFF3 file expressed in BED's 0-based half-open coordinates, where the start is one lower and the end is unchanged. Confusing the two conventions shifts every interval by a base, and this pair makes that shift a visible diff.
NXCTG01 100 460 gene0001 960 +
NXCTG01 100 220 exon0001 900 +
NXCTG01 300 460 exon0002 900 +
NXCTG01 120 220 cds0001 850 +
NXCTG01 300 420 cds0002 850 +
NXCTG01 500 580 gene0002 700 -
Specifications
- Format
- BED6
- Intervals
- 6
- Columns
- 6
- Coordinate System
- 0-based half-open
- Same Features As
- the GFF3 annotations
- Score Range
- 700 to 960
- Off By One Rule
- bedStart = gffStart - 1, bedEnd = gffEnd
Testing contract
Expected to pass- Scenario
- Convert every interval here to 1-based inclusive coordinates and compare against the matching GFF3 feature.
- Expected result
- Adding one to each start reproduces the GFF3 coordinates exactly while the ends already match, and every interval length is identical under both conventions.
What is a .bed file?
BED is a tab-delimited format for genomic intervals. The first three columns — chromosome, 0-based start, and exclusive end — are required, and up to nine optional columns add name, score, strand, thick-drawn range, colour, and block (exon) structure. The half-open, zero-based coordinate convention is the single most common source of off-by-one errors when converting to or from GFF3 and other 1-based formats.
How to use this file
Use an example .bed file to test interval parsers, overlap and intersection tools, and coordinate converters, verifying the half-open convention, correct handling of the optional trailing columns, and that track and browser header lines are skipped.
How to use this file for testing
“BED6 Intervals — 0-Based Half-Open Coordinates (.bed)” is a deterministic Novus Examples fixture for Scientific data, Editor testing. Citation catalogs (BibTeX, RIS), chemistry structures (MDL Molfile, PDB), and gridded binary data (NetCDF, FITS) — for testing reference managers, molecule viewers, and scientific-data loaders.
Documented properties for this file: 6 columns · BED6. Compare results against paired or grouped companions on this page when present (clean↔damaged, searchable↔scanned, or format twins) so scores stay reproducible across runs.
Download the file once, keep the path stable in CI or local scripts, and treat the spec table as the contract: dimensions, seeds, field lists, and roles are intentional. Corrupt or invalid samples are labelled as such — expect parsers to fail loudly rather than silently accept them.
Scientific fixtures are small, valid, and fully synthetic — no real organism, patient, sample, or observation. Point your parser or loader at the file and check it reads the documented records, variables, or headers; binary formats ship a readable twin or metadata listing for comparison.
Related files
- fastaFASTA Contigs — One Line Per Record (.fasta)The same four contigs written one sequence per line rather than wrapped, which is how many pipelines emit FASTA and how many line-oriented parsers assume it always looks. Comparing against the wrapped twin proves a parser joins continuation lines instead of taking the first one.
- fastaFASTA Contigs — Wrapped at 60 Columns (.fasta)Four 600-base synthetic contigs wrapped at the conventional 60 columns, with the length and an invented organism name in each header. The sequences come from a fixed seed, so they are reproducible and belong to nothing that exists.
- csvFASTQ Quality Score Reference — Both Encodings Decoded (.csv)Every twelfth base of the six reads with its Phred score, the ASCII character it takes under both offsets, and the error probability that score implies. It converts a quality-encoding argument into a lookup you can diff.
- fastqFASTQ Reads — Phred+33 (Sanger / Illumina 1.8+) (.fastq)Six 60-base reads with Phred+33 quality strings, the modern Sanger encoding used by everything since Illumina 1.8. Quality declines along each read the way real sequencing does, so a mis-decoded offset produces implausible scores rather than plausible ones.
- fastqFASTQ Reads — Phred+64 Legacy Encoding (.fastq)The identical reads and identical quality scores written with the legacy Phred+64 offset used by older Illumina pipelines. Decode it with the modern offset and every base looks 31 points better than it is, which is a silent quality inflation rather than a parse failure.
- fastqIntentionally Corrupt FASTQ — Final Record Missing Its Quality Line (.fastq)An intentionally corrupt FASTQ whose first five records are complete and whose sixth ends after the plus line, leaving no quality string. A four-line-block reader must report an incomplete final record rather than pairing the sequence with an empty quality string.
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