PRJNA175449

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

Onion bulk RNA-seq (454 pyrosequencing). Completely unsuitable for reuse (grade F). Catastrophic failure on both Q30 (29%, scored 0/100) and mean base quality (10.8, scored 0/100)—seven of ten bases are below Q20, rendering transcript abundance and isoform discovery unfeasible.

Data type / assay

bulk-RNA-seq

Organism

Allium cepa

Instrument

454 GS FLX Titanium

Platform

LS454

Files available

FASTQ (raw reads)

N numbers (samples, groups)

6 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 2036430155 reported

total reads 3600352 reported

n content pct 0.071 measured

pct q20 bases 29 measured

pct q30 bases 29 measured

gc content pct 42.2 measured

mean read length 313.2 measured

mean base quality 10.8 measured

adapter content pct 0 measured

duplication rate pct 26.89 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 33/100

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

pct q30 bases 29 measured ×1 0%

mean base quality 10.8 measured ×0.6 0%

adapter content pct 0 measured ×0.4 100%

duplication rate pct 26.89 measured ×0.4 100%

QC cost 26 s compute

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