SRR12763566

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

51/100 · F

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

What this means

claude:haiku

Short-read Illumina amplicon of SARS-CoV-2. Grade F (51/100): only failing sample in batch, not recommended for reuse. Reduced Q30 bases (85.4%, scoring 77/100, weight 1) combined with adapter contamination (19.16%, scoring 0/100) create a compounding quality deficit unsuitable for reliable variant calling.

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 324609684 reported

total reads 1111677 reported

n content pct 0 measured

pct q20 bases 94.8 measured

pct q30 bases 85.4 measured

gc content pct 39.5 measured

mean read length 146 measured

mean base quality 34.5 measured

adapter content pct 19.16 measured

duplication rate pct 80.08 measured

How this grade was computed

Weighted mean of 2 scored metric(s) → 51/100

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 85.4 measured ×1 77%

adapter content pct 19.16 measured ×0.5 0%

QC cost 36 s compute

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