SRR12763552

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

28/100 · 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 on NovaSeq 6000 with ~1.7M reads but notably lower Q30 (78.3%) and Q20 (90.6%), suggesting possible cluster density issues or chemistry variability. Use cautiously for variant calling; consensus sequences may tolerate lower quality better than SNV detection.

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 507027340 reported

total reads 1736395 reported

n content pct 0 measured

pct q20 bases 90.6 measured

pct q30 bases 78.3 measured

gc content pct 39.5 measured

mean read length 146 measured

mean base quality 33.1 measured

adapter content pct 22.02 measured

duplication rate pct 75.91 measured

How this grade was computed

Weighted mean of 2 scored metric(s) → 28/100

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 78.3 measured ×1 42%

adapter content pct 22.02 measured ×0.5 0%

QC cost 23 s compute

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