PRJNA645024

BioProject first seen 2021

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

39/100 · 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 HiSeq 2000 exome capture (WES) of porcine genome with 287.6M reads but reduced base quality (78% Q20, 66.5% Q30), limiting variant confidence for sensitive SNP applications. Suitable for broader interrogation of protein-coding regions with relaxed accuracy requirements.

Data type / assay

WES

Organism

Sus scrofa

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 83523295200 reported

total reads 287580932 reported

n content pct 0.016 measured

pct q20 bases 78 measured

pct q30 bases 66.5 measured

gc content pct 54.7 measured

mean read length 150 measured

mean base quality 32 measured

adapter content pct 96.66 measured

duplication rate pct 61.1 measured

mean target coverage 1670.5 extrapolated

How this grade was computed

Weighted mean of 4 scored metric(s) → 39/100

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 1670.5 extrapolated ×1.2 100%

pct q30 bases 66.5 measured ×1 0%

duplication rate pct 61.1 measured ×0.5 0%

adapter content pct 96.66 measured ×0.4 0%

QC cost 30 s compute

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