PRJEB2839

BioProject first seen 2016

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

100/100 · A

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

What this means

claude:haiku

Streptococcus agalactiae (Group B Streptococcus, GBS) whole-genome sequencing via Illumina HiSeq 2000 with 869.7 million reads and 173.9 billion bases at good quality (96.5% Q20, 90.1% Q30). The low GC (39.2%) is characteristic of this gram-positive bacterium. This large dataset supports population genetics, serotype identification, and virulence factor discovery in this major maternal-fetal pathogen.

Data type / assay

WGS

Organism

Streptococcus agalactiae

Instrument

Illumina HiSeq 2000

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads), BAM/CRAM (aligned)

N numbers (samples, groups)

508 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 173948077000 reported

total reads 869740385 reported

n content pct 0.014 measured

pct q20 bases 96.5 measured

pct q30 bases 90.1 measured

gc content pct 39.2 measured

mean read length 100 measured

mean base quality 37.8 measured

adapter content pct 0.01 measured

duplication rate pct 7.14 measured

How this grade was computed

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

The A 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 90.1 measured ×1 100%

duplication rate pct 7.14 measured ×0.5 100%

adapter content pct 0.01 measured ×0.4 100%

QC cost 7 s compute

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