SRX1766927

SRA

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

84/100 · B

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

What this means

claude:haiku

Whole-genome sequencing of *Shigella sonnei* via Illumina HiSeq 2500 with limited depth (1.6M reads, ~200x coverage) but exceptional quality (99% Q20, 94.3% Q30). Adequate depth for accurate SNP and small-indel calling; particularly useful for outbreak tracking and antimicrobial resistance surveillance.

Data type / assay

WGS

Organism

Shigella sonnei

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 314007864 reported

total reads 1586984 reported

n content pct 0.002 measured

pct q20 bases 99 measured

pct q30 bases 94.3 measured

gc content pct 49.6 measured

mean read length 99.3 measured

mean base quality 36.3 measured

adapter content pct 1.1 measured

duplication rate pct 27.23 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 84/100

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 94.3 measured ×1 100%

duplication rate pct 27.23 measured ×0.5 40%

adapter content pct 1.1 measured ×0.4 99%

QC cost 19 s compute

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