PRJNA209484

BioProject first seen 2013

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

38/100 · F

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

What this means

claude:haiku

Illumina Genome Analyzer II whole-exome capture (WXS) of Homo sapiens delivers 1.9 billion bases from 12.5 million reads at 83.7% Q20. Older chemistry with moderate accuracy; adequate for exome-based variant discovery but elevated false-positive SNP rate versus modern sequencers.

Data type / assay

WES

Organism

Homo sapiens

Instrument

Illumina Genome Analyzer II

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

15 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 1874982000 reported

total reads 12499880 reported

n content pct 0.035 measured

pct q20 bases 83.7 measured

pct q30 bases 77.3 measured

gc content pct 43.1 measured

mean read length 75 measured

mean base quality 31.5 measured

adapter content pct 0 measured

duplication rate pct 74.05 measured

mean target coverage 30.2 extrapolated

How this grade was computed

Weighted mean of 4 scored metric(s) → 38/100

The F grade is a transparent weighted average. Each metric below scored from 0–100% against the published WES thresholds, weighted by its importance; nothing is hidden or subjective.

mean target coverage 30.2 extrapolated ×1.2 34%

pct q30 bases 77.3 measured ×1 37%

duplication rate pct 74.05 measured ×0.5 0%

adapter content pct 0 measured ×0.4 100%

QC cost 6 s compute

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