SRR5585309

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

89/100 · B

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

What this means

claude:haiku

Bacterial WGS with strong base quality (Q30 95.6%, mean 37.9) and zero adapter contamination, but elevated duplication (21.07%) moderately reduces variant confidence, particularly for low-frequency mutations. Grade B indicates borderline reusability; acceptable for primary assembly but consider supplemental sequencing for variant refinement.

Data type / assay

WGS

Organism

Salmonella enterica subsp. enterica serovar Haifa

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 341484838 reported

total reads 1745684 reported

n content pct 0.017 measured

pct q20 bases 97.5 measured

pct q30 bases 95.6 measured

gc content pct 51 measured

mean read length 97.8 measured

mean base quality 37.9 measured

adapter content pct 0 measured

duplication rate pct 21.07 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 89/100

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 95.6 measured ×1 100%

duplication rate pct 21.07 measured ×0.5 59%

adapter content pct 0 measured ×0.4 100%

QC cost 14 s compute

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