SRP005622

SRA first seen 2012

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

41/100 · F

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

What this means

claude:haiku

Homo sapiens whole-genome sequencing on HiSeq 2000 yielding 45.2 billion bases (~14.6x extrapolated coverage, 73.4% Q20), providing human genetic variation data but with notably lower quality metrics (63% Q30) than contemporary standards; elevated N-content (2.685%) suggests technical difficulties during sequencing.

Data type / assay

WGS

Organism

Homo sapiens

Instrument

Illumina HiSeq 2000

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

2 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 45215656770 reported

total reads 223839885 reported

mean coverage 14.6 extrapolated

n content pct 2.685 measured

pct q20 bases 73.4 measured

pct q30 bases 63 measured

gc content pct 41.8 measured

mean read length 101 measured

mean base quality 25.9 measured

adapter content pct 0.07 measured

duplication rate pct 2.72 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 41/100

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.

mean coverage 14.6 extrapolated ×1.2 30%

pct q30 bases 63 measured ×1 0%

duplication rate pct 2.72 measured ×0.5 100%

adapter content pct 0.07 measured ×0.4 100%

QC cost 38 s compute

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