PRJEB23993

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

78/100 · C

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

What this means

claude:haiku

Escherichia coli WGS with critical liabilities including high adapter contamination (28.4%—indicative of poor library preparation) and below-optimal Q30 (84.4%); provisional grade (evidence 0.61) with highly extrapolated coverage (37,122×) requires aggressive trimming and remapping validation before variant calling.

Data type / assay

WGS

Organism

Escherichia coli

Instrument

Illumina HiSeq 4000

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads), submitted files

N numbers (samples, groups)

368 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 170765435795 reported

total reads 437401308 reported

mean coverage 37122.9 extrapolated

n content pct 0.001 measured

pct q20 bases 91.7 measured

pct q30 bases 84.4 measured

gc content pct 50.2 measured

mean read length 301 measured

mean base quality 34.2 measured

adapter content pct 28.4 measured

duplication rate pct 7.89 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 78/100

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.

mean coverage 37122.9 extrapolated ×1.2 100%

pct q30 bases 84.4 measured ×1 72%

duplication rate pct 7.89 measured ×0.5 100%

adapter content pct 28.4 measured ×0.4 0%

QC cost 6 s compute

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