PRJNA888402

BioProject first seen 2023

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

71/100 · C

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

What this means

claude:haiku

SARS-CoV-2 hybrid amplicon sequencing via HiSeq 2500 from 41 samples reaching 94.1 billion bases (97.4% Q20), enabling high-volume pathogen surveillance with both short and long reads for consensus genome and variant detection.

Data type / assay

amplicon

Organism

Severe acute respiratory syndrome coronavirus 2

Instrument

Illumina HiSeq 2500

Platform

ILLUMINA

Read type

hybrid (short+long)

Files available

FASTQ (raw reads)

N numbers (samples, groups)

41 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 94136317852 reported

total reads 1174822648 reported

n content pct 0 measured

pct q20 bases 97.4 measured

pct q30 bases 94.7 measured

gc content pct 42.8 measured

mean read length 50 measured

mean base quality 33.2 measured

adapter content pct 13.19 measured

duplication rate pct 96.57 measured

How this grade was computed

Weighted mean of 2 scored metric(s) → 71/100

The C grade is a transparent weighted average. Each metric below scored from 0–100% against the published amplicon thresholds, weighted by its importance; nothing is hidden or subjective.

pct q30 bases 94.7 measured ×1 100%

adapter content pct 13.19 measured ×0.5 13%

QC cost 48 s compute

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