SRR12661018

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

69/100 · 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, Illumina NovaSeq. D-grade (69/100) with problematic adapter content (13.85%) paired with high duplication (92%), signaling combined library and template quality issues. Q30 (97%) is the bright spot, but adapter carryover will introduce off-target sequences that confound variant calls; reuse requires aggressive preprocessing and results validation.

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 472962036 reported

total reads 1619733 reported

n content pct 0 measured

pct q20 bases 99.2 measured

pct q30 bases 97 measured

gc content pct 39.9 measured

mean read length 146 measured

mean base quality 36.5 measured

adapter content pct 13.85 measured

duplication rate pct 91.97 measured

How this grade was computed

Weighted mean of 2 scored metric(s) → 69/100

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 97 measured ×1 100%

adapter content pct 13.85 measured ×0.5 8%

QC cost 28 s compute

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