PRJEB12658

BioProject first seen 2018

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

95/100 · A

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

What this means

claude:haiku

Niallia circulans WGS constrained mainly by modest adapter contamination (4.4%) despite otherwise excellent metrics (Q30 93.6%, duplication 7.95%); well-suited for genome assembly and variant calling provided standard adapter-trimming preprocessing is applied.

Data type / assay

WGS

Organism

Niallia circulans

Instrument

Illumina Genome Analyzer IIx

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads), submitted files

N numbers (samples, groups)

1 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 417303902 reported

total reads 1381801 reported

n content pct 0.027 measured

pct q20 bases 95.3 measured

pct q30 bases 93.6 measured

gc content pct 52.5 measured

mean read length 151 measured

mean base quality 36.2 measured

adapter content pct 4.41 measured

duplication rate pct 7.95 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 95/100

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 93.6 measured ×1 100%

duplication rate pct 7.95 measured ×0.5 100%

adapter content pct 4.41 measured ×0.4 76%

QC cost 15 s compute

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