PRJNA517575

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

93/100 · A

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

What this means

claude:haiku

HiSeq 2500 whole-genome sequencing of Escherichia coli with 417 million short reads and extreme 7,362× mean coverage of 33.9 Gb at high quality (96.4% Q20, 94.4% Q30). Exceptional depth far exceeds typical bacterial genome needs; useful for benchmarking variant-calling algorithms and validation workflows.

Data type / assay

WGS

Organism

Escherichia coli

Instrument

Illumina HiSeq 2500

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

72 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 33865609127 reported

total reads 416973501 reported

mean coverage 7362.1 extrapolated

n content pct 0.012 measured

pct q20 bases 96.4 measured

pct q30 bases 94.4 measured

gc content pct 50.9 measured

mean read length 150 measured

mean base quality 37.6 measured

adapter content pct 3.8 measured

duplication rate pct 16.9 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 93/100

The A 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 7362.1 extrapolated ×1.2 100%

pct q30 bases 94.4 measured ×1 100%

duplication rate pct 16.9 measured ×0.5 72%

adapter content pct 3.8 measured ×0.4 80%

QC cost 21 s compute

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