Corpus 1,273 assessed · 1,174 scored · 643 reproduced ≥75 · 169 flagged ·∅ 74.1/100
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PRJEB11579

BioProject first seen 2016

Provenance — who produced it, who reused it

Linked to 1 papers in the literature. Roles are inferred factual signals (who deposited the data vs who reused it), with counts — never a judgement about any author.

Reused by

1 further paper cites this accession but reuse could not be confirmed.

Deep data QC

33/100 · F

Standardized, field-standard QC computed by touching the data — every metric states how it was obtained · evidence: measured

What this means
claude:haiku

This Homo sapiens amplicon dataset from Ion Torrent PGM provides targeted coverage (62 million reads, GC=45.3%) at modest per-base accuracy (Q30=50.6%)—Ion Torrent's systematic homopolymer biases may distort indel rates in microsatellite regions, best suited for large targeted variant sets where high depth compensates for lower per-base fidelity or for genotyping single-nucleotide polymorphisms where indel calling is not critical.

Data type / assay
amplicon
Organism
Homo sapiens
Instrument
Ion Torrent PGM
Platform
ION_TORRENT
Read type
short-read
Files available
FASTQ (raw reads), BAM/CRAM (aligned)
N numbers (samples, groups)
234 runs
Metrics (value · how obtained)
checksum ok yes reported
total bases 4665111144 reported
total reads 62892380 reported
n content pct 0 measured
pct q20 bases 82.6 measured
pct q30 bases 50.6 measured
gc content pct 45.3 measured
mean read length 71.1 measured
mean base quality 27.3 measured
adapter content pct 0 measured
duplication rate pct 74.86 measured
mean target coverage 75.2 extrapolated
How this grade was computed
Weighted mean of 2 scored metric(s) → 33/100

The F grade is a transparent weighted average. Each metric below scored from 0–100% against the published amplicon thresholds, weighted by its importance; nothing is hidden or subjective.

pct q30 bases 50.6 measured ×1 0%
adapter content pct 0 measured ×0.5 100%
QC cost 3 s compute

measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0