PRJNA53773

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

44/100 · F

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

What this means

claude:haiku

Legacy 454 WGS of Staphylococcus epidermidis with marginal base quality. Q30 at 67.4% (weight-1 metric, scored 0/100) falls below acceptable thresholds for variant calling, compounded by modest duplication (12.21%). Grade-F verdict reflects aging data unsuitable for high-confidence SNP discovery without orthogonal validation.

Data type / assay

WGS

Organism

Staphylococcus epidermidis VCU129

Instrument

454 GS FLX Titanium

Platform

LS454

Files available

FASTQ (raw reads)

N numbers (samples, groups)

1 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 68080590 reported

total reads 139934 reported

n content pct 0.018 measured

pct q20 bases 87.4 measured

pct q30 bases 67.4 measured

gc content pct 33.5 measured

mean read length 334.8 measured

mean base quality 32.1 measured

adapter content pct 0 measured

duplication rate pct 12.21 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 44/100

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

pct q30 bases 67.4 measured ×1 0%

duplication rate pct 12.21 measured ×0.5 87%

adapter content pct 0 measured ×0.4 100%

QC cost 18 s compute

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