SRR1960126

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 Braenderup). Grade B—duplication and adapter jointly limiting. Measured duplication (19.63%, component score 64/100) and adapter content (2.98%, component score 86/100) represent moderate contamination risk; Q30 (94.8%, measured) is solid. Trim and filter conservatively for rare-variant discovery.

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 325158134 reported

total reads 1643086 reported

n content pct 0.007 measured

pct q20 bases 99 measured

pct q30 bases 94.8 measured

gc content pct 51.9 measured

mean read length 99.3 measured

mean base quality 36.4 measured

adapter content pct 2.98 measured

duplication rate pct 19.63 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 94.8 measured ×1 100%

duplication rate pct 19.63 measured ×0.5 64%

adapter content pct 2.98 measured ×0.4 86%

QC cost 26 s compute

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