SRR3048688

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

75/100 · C

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

What this means

claude:haiku

Salmonella enterica serovar Braenderup whole-genome short-read sequencing on HiSeq 2500 (1.2M reads, 230M bases, 99.9% Q20, 99.1% Q30). The near-perfect base quality enables accurate SNP calling but the shallow depth (~3-4× coverage assuming ~5 Mb genome) limits structural variant detection and requires careful assembly strategies.

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 230189130 reported

total reads 1187907 reported

n content pct 0 measured

pct q20 bases 99.9 measured

pct q30 bases 99.1 measured

gc content pct 51.2 measured

mean read length 98.1 measured

mean base quality 37.4 measured

adapter content pct 10.08 measured

duplication rate pct 22.04 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 75/100

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 99.1 measured ×1 100%

duplication rate pct 22.04 measured ×0.5 56%

adapter content pct 10.08 measured ×0.4 35%

QC cost 1 min compute

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