SRR1958349

SRA first seen 2021

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

87/100 · B

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

What this means

claude:haiku

WGS short-read (Salmonella). Grade B—acceptable for variant calling but duplication-limited. Duplication at 21.5% (measured, component score 58/100) is the primary drag and elevates false-positive risk for rare-variant discovery; adapter content (2%, scored 93/100) is minor. Use with variant filtering for low-allele-fraction calls.

Data type / assay

WGS

Organism

Salmonella enterica subsp. enterica serovar Braenderup

Instrument

Illumina HiSeq 2500

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

1 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 303818507 reported

total reads 1587717 reported

n content pct 0 measured

pct q20 bases 99.9 measured

pct q30 bases 98.5 measured

gc content pct 52 measured

mean read length 97.2 measured

mean base quality 37.1 measured

adapter content pct 2 measured

duplication rate pct 21.46 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 87/100

The B 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 98.5 measured ×1 100%

duplication rate pct 21.46 measured ×0.5 58%

adapter content pct 2 measured ×0.4 93%

QC cost 38 s compute

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