PRJEB27826

BioProject first seen 2019

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

79/100 · C

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

What this means

claude:haiku

Listeria innocua WGS severely limited by extreme duplication rate (33.4%) far exceeding typical bacterial expectations and suggesting PCR bias or low-complexity input; despite good base quality (Q30 94.9%), the high duplication compromises copy-number inference and de novo assembly reliability.

Data type / assay

WGS

Organism

Listeria innocua

Instrument

NextSeq 500

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads), submitted files

N numbers (samples, groups)

6 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 1859784723 reported

total reads 6404570 reported

n content pct 0.002 measured

pct q20 bases 97.3 measured

pct q30 bases 94.9 measured

gc content pct 40.6 measured

mean read length 149.8 measured

mean base quality 34.7 measured

adapter content pct 0 measured

duplication rate pct 33.38 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 79/100

The C 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 94.9 measured ×1 100%

duplication rate pct 33.38 measured ×0.5 21%

adapter content pct 0 measured ×0.4 100%

QC cost 6 s compute

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