Corpus 1,273 assessed · 1,174 scored · 643 reproduced ≥75 · 169 flagged ·∅ 74.1/100
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PRJNA420081

BioProject first seen 2020

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

67/100 · D

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

What this means
claude:haiku

Targeted WES of Lepus americanus. Grade D (67/100) — marginal for exome sequencing. Q30 bases at 77.4% (measured, scored 37/100) fall significantly below the 90%+ standard for reliable variant calling; mean quality (31, measured) is moderate, compromising sensitivity for heterozygous and rare variants, and stringent filtering will be required to distinguish true variants from sequencing artifacts.

Data type / assay
WES
Organism
Lepus americanus
Instrument
Illumina HiSeq 1500
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
270 runs
Metrics (value · how obtained)
checksum ok yes reported
total bases 1023189968508 reported
total reads 4101192548 reported
n content pct 0.019 measured
pct q20 bases 83.9 measured
pct q30 bases 77.4 measured
gc content pct 44.4 measured
mean read length 100 measured
mean base quality 31 measured
adapter content pct 0.12 measured
duplication rate pct 1.13 measured
How this grade was computed
Weighted mean of 3 scored metric(s) → 67/100

The D 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.

pct q30 bases 77.4 measured ×1 37%
duplication rate pct 1.13 measured ×0.5 100%
adapter content pct 0.12 measured ×0.4 100%
QC cost 33 s compute

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