SRR12763507

SRA 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

60/100 · D

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

What this means

claude:haiku

SARS-CoV-2 amplicon sequencing; not recommended for reuse (grade D). Elevated adapter contamination (20.59%, scored 0/100) combined with lower Q30 content (87.9%, scored 90/100) jointly compromise amplicon targeting fidelity and base-level confidence. The dual quality concerns create downstream uncertainty in SNP/indel detection, warranting either intensive re-processing or dataset exclusion.

Data type / assay

amplicon

Organism

Severe acute respiratory syndrome coronavirus 2

Instrument

Illumina NovaSeq 6000

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

1 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 659646104 reported

total reads 2259062 reported

n content pct 0.002 measured

pct q20 bases 92.5 measured

pct q30 bases 87.9 measured

gc content pct 39 measured

mean read length 146 measured

mean base quality 33.3 measured

adapter content pct 20.59 measured

duplication rate pct 86.74 measured

How this grade was computed

Weighted mean of 2 scored metric(s) → 60/100

The D 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 87.9 measured ×1 90%

adapter content pct 20.59 measured ×0.5 0%

QC cost 36 s compute

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