PRJNA953810

BioProject

Provenance — who produced it, who reused it

Linked to 0 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.

No linked papers found in the corpus yet.

Deep data QC

77/100 · C

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

What this means

claude:haiku

Bulk RNA-seq with contradictory metrics: reported perfect Q20/Q30 despite mean base quality of only 30, the true limiting factor; moderate-to-high duplication (48%) compounds low actual base accuracy; low mean base quality makes this dataset risky for reliable quantification.

Data type / assay

bulk-RNA-seq

Organism

Mus musculus

Instrument

NextSeq 550

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

79 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 408633176928 reported

total reads 2688376164 reported

n content pct 0.001 measured

pct q20 bases 100 measured

pct q30 bases 100 measured

gc content pct 51.4 measured

mean read length 76 measured

mean base quality 30 measured

adapter content pct 0.18 measured

duplication rate pct 48.03 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 77/100

The C 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 0.18 measured ×0.4 100%

duplication rate pct 48.03 measured ×0.4 60%

QC cost 21 s compute

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