SRR12661060

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

58/100 · F

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

What this means

claude:haiku

SARS-CoV-2 amplicon, Illumina NovaSeq. Fails QC (F, 58/100) due to catastrophic adapter contamination (20.98%), indicating incomplete primer removal or ligation failures that will generate off-target reads and chimeras. Q30 bases (87.5%) are respectable but cannot rescue a dataset where ~21% of reads carry unwanted sequence; reuse not recommended without aggressive remediation and revalidation.

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 688985096 reported

total reads 2359538 reported

n content pct 0 measured

pct q20 bases 95.7 measured

pct q30 bases 87.5 measured

gc content pct 39.2 measured

mean read length 146 measured

mean base quality 34.9 measured

adapter content pct 20.98 measured

duplication rate pct 84.46 measured

How this grade was computed

Weighted mean of 2 scored metric(s) → 58/100

The F 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 87.5 measured ×1 88%

adapter content pct 20.98 measured ×0.5 0%

QC cost 20 s compute

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