PRJNA412424

BioProject

Provenance — who produced it, who reused it

Linked to 0 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.

No linked papers found in the corpus yet.

Deep data QC

87/100 · B

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

What this means

claude:haiku

Chicken WGS with excellent extrapolated coverage (305.3×) but Q30 base quality of only 82% limits variant-calling sensitivity and false-discovery control. Evidence is provisional due to extrapolated coverage; measured-depth confirmation is pending.

Data type / assay

WGS

Organism

Gallus gallus

Instrument

Illumina HiSeq 2000

Platform

ILLUMINA

Read type

hybrid (short+long)

Files available

FASTQ (raw reads)

N numbers (samples, groups)

18 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 335825774942 reported

total reads 1201372148 reported

mean coverage 305.3 extrapolated

n content pct 0 measured

pct q20 bases 92.6 measured

pct q30 bases 82 measured

gc content pct 41.5 measured

mean read length 139.1 measured

mean base quality 33.3 measured

adapter content pct 0 measured

duplication rate pct 0.52 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 87/100

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.

mean coverage 305.3 extrapolated ×1.2 100%

pct q30 bases 82 measured ×1 60%

duplication rate pct 0.52 measured ×0.5 100%

adapter content pct 0 measured ×0.4 100%

QC cost 12 s compute

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