PRJEB2968

BioProject

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

100/100 · A

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

What this means

claude:haiku

Whole-genome resequencing of *Escherichia coli* via Illumina HiSeq 2000 with exceptional depth (~6935x coverage) and high quality (98.4% Q20), enabling sensitive SNP detection and strain differentiation. Extreme depth suitable for calling rare variants or assessing microdiversity but exceeds typical requirements for single-isolate sequencing.

Data type / assay

WGS

Organism

Escherichia coli

Instrument

Illumina HiSeq 2000

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads), BAM/CRAM (aligned)

N numbers (samples, groups)

96 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 31901633000 reported

total reads 159508165 reported

mean coverage 6935.1 extrapolated

n content pct 0.006 measured

pct q20 bases 98.4 measured

pct q30 bases 93.1 measured

gc content pct 50.5 measured

mean read length 100 measured

mean base quality 36 measured

adapter content pct 0.04 measured

duplication rate pct 3.67 measured

How this grade was computed

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

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 6935.1 extrapolated ×1.2 100%

pct q30 bases 93.1 measured ×1 100%

duplication rate pct 3.67 measured ×0.5 100%

adapter content pct 0.04 measured ×0.4 100%

QC cost 17 s compute

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