PRJNA227254

BioProject first seen 2014

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

88/100 · B

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

What this means

claude:haiku

Plasmodium vivax WGS with good measured quality (B grade). Q30 at 95.5% is strong, but duplication at 22.69% moderately degrades sensitivity for rare variants and assembly contiguity. Acceptable for routine resequencing; quantify duplication impact before claiming full variant discovery confidence.

Data type / assay

WGS

Organism

Plasmodium vivax

Instrument

Illumina HiSeq 2000

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

14 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 31338291000 reported

total reads 156691455 reported

n content pct 0.011 measured

pct q20 bases 97.5 measured

pct q30 bases 95.5 measured

gc content pct 45.6 measured

mean read length 100 measured

mean base quality 36.5 measured

adapter content pct 0.06 measured

duplication rate pct 22.69 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 88/100

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 95.5 measured ×1 100%

duplication rate pct 22.69 measured ×0.5 54%

adapter content pct 0.06 measured ×0.4 100%

QC cost 27 s compute

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