PRJNA143627

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

83/100 · B

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

What this means

claude:haiku

Gallus gallus bulk RNA-seq (Genome Analyzer IIx); grade B—usable but with caveats. Mean base quality of 30 (scored 33/100) is the limiting factor despite Q20 and Q30 appearing perfect, and elevated N-content (0.682%) suggests sequencing artifacts; Q30 of 100% provides a foundation, but aggressive quality filtering is recommended before transcript quantification.

Data type / assay

bulk-RNA-seq

Organism

Gallus gallus

Instrument

Illumina Genome Analyzer IIx

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

149 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 296903362282 reported

total reads 3558696916 reported

n content pct 0.682 measured

pct q20 bases 100 measured

pct q30 bases 100 measured

gc content pct 51.5 measured

mean read length 76 measured

mean base quality 30 measured

adapter content pct 0.78 measured

duplication rate pct 14.01 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 83/100

The B 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 100 measured ×1 100%

mean base quality 30 measured ×0.6 33%

adapter content pct 0.78 measured ×0.4 100%

duplication rate pct 14.01 measured ×0.4 100%

QC cost 36 s compute

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