SRR1961909

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

70/100 · C

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

What this means

claude:haiku

WGS short-read (Salmonella Sinstorf). Grade C—problematic adapter contamination. Measured adapter content of 16.23% (component score 0/100) is the critical failure, indicating incomplete library prep or input contamination; duplication (18.31%, measured) and Q30 (96.7%, measured) are otherwise acceptable. Aggressive trimming required before variant calling.

Data type / assay

WGS

Organism

Salmonella enterica subsp. enterica serovar Sinstorf

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 248297774 reported

total reads 1255958 reported

n content pct 0 measured

pct q20 bases 99.4 measured

pct q30 bases 96.7 measured

gc content pct 51.9 measured

mean read length 99.5 measured

mean base quality 36.9 measured

adapter content pct 16.23 measured

duplication rate pct 18.31 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 70/100

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 96.7 measured ×1 100%

duplication rate pct 18.31 measured ×0.5 68%

adapter content pct 16.23 measured ×0.4 0%

QC cost 9 s compute

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