PRJEB22893

BioProject

Provenance — who produced it, who reused it

Linked to 4 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

4 further papers cite this accession but reuse could not be confirmed.

Deep data QC

93/100 · A

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

What this means

claude:haiku

Human whole-genome sequencing via Illumina HiSeq 2000 with good depth (398M reads, ~25.9x coverage) and exceptional quality (99.4% Q20, 98.9% Q30), suitable for variant discovery and population studies. Quality and depth combination support reliable SNP and small indel calling across the genome.

Data type / assay

WGS

Organism

Homo sapiens

Instrument

Illumina HiSeq 2000

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads), submitted files

N numbers (samples, groups)

25 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 80277705384 reported

total reads 398245184 reported

mean coverage 25.9 extrapolated

n content pct 0 measured

pct q20 bases 99.4 measured

pct q30 bases 98.9 measured

gc content pct 46.7 measured

mean read length 100.6 measured

mean base quality 39.1 measured

adapter content pct 0 measured

duplication rate pct 1.43 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 93/100

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.

mean coverage 25.9 extrapolated ×1.2 81%

pct q30 bases 98.9 measured ×1 100%

duplication rate pct 1.43 measured ×0.5 100%

adapter content pct 0 measured ×0.4 100%

QC cost 18 s compute

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