SRR12763532

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

62/100 · 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; marginal quality (grade D). Elevated adapter contamination (24.91%, scored 0/100) combined with lower-end base quality (Q30: 88.7%, scored 94/100) create dual quality concerns that significantly increase downstream risk for variant detection errors. This run warrants either intensive re-trimming or exclusion from consensus-based analyses.

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 220167124 reported

total reads 753997 reported

n content pct 0 measured

pct q20 bases 96.1 measured

pct q30 bases 88.7 measured

gc content pct 40.3 measured

mean read length 146 measured

mean base quality 35.1 measured

adapter content pct 24.91 measured

duplication rate pct 86.66 measured

How this grade was computed

Weighted mean of 2 scored metric(s) → 62/100

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 88.7 measured ×1 94%

adapter content pct 24.91 measured ×0.5 0%

QC cost 13 s compute

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