PRJNA227106

BioProject first seen 2020

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

54/100 · F

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

What this means

claude:haiku

Apilactobacillus kunkeei WGS (Genome Analyzer II); grade F—marginal for variant calling. Q30 of 78% is insufficient for high-confidence SNP detection without aggressive filtering, and adapter content (5.44%) adds systematic noise. Older sequencer platform compounds these issues.

Data type / assay

WGS

Organism

Apilactobacillus kunkeei EFB6

Instrument

Illumina Genome Analyzer II

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 1837249120 reported

total reads 8202005 reported

n content pct 0.084 measured

pct q20 bases 89.6 measured

pct q30 bases 78 measured

gc content pct 37.8 measured

mean read length 112 measured

mean base quality 31.9 measured

adapter content pct 5.44 measured

duplication rate pct 17.95 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 54/100

The F 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 78 measured ×1 40%

duplication rate pct 17.95 measured ×0.5 69%

adapter content pct 5.44 measured ×0.4 68%

QC cost 22 s compute

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