SRP065057

ENA 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

71/100 · C

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

What this means

claude:haiku

Aspen whole-genome sequencing with borderline base quality. Marginal QC (71/100, C) with Q30 of 79.8%, falling below the ~85% standard needed for confident variant calling, and elevated adapter content (2.72%) suggesting incomplete library preparation; both metrics increase false-variant rates. Usable for genome assembly but risky for variant discovery.

Data type / assay

WGS

Organism

Populus tremula

Instrument

Illumina HiSeq 2000

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

95 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 1403676987556 reported

total reads 6990857572 reported

n content pct 0.2 measured

pct q20 bases 87.6 measured

pct q30 bases 79.8 measured

gc content pct 36.6 measured

mean read length 100 measured

mean base quality 32.3 measured

adapter content pct 2.72 measured

duplication rate pct 3.89 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 71/100

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 79.8 measured ×1 49%

duplication rate pct 3.89 measured ×0.5 100%

adapter content pct 2.72 measured ×0.4 88%

QC cost 34 s compute

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