SRR12833559

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

67/100 · 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 short-read amplicon. Grade D; evidence provisional. Lowest adapter content in amplicon cohort (18.08%) but still scored zero; trimming required. Q30 at 96% is excellent. Largest read count (3.7M) among amplicons provides excellent depth for consensus or low-frequency variant detection once adapters are removed.

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 1094592076 reported

total reads 3748603 reported

n content pct 0.001 measured

pct q20 bases 98.8 measured

pct q30 bases 96 measured

gc content pct 38.9 measured

mean read length 146 measured

mean base quality 36.3 measured

adapter content pct 18.08 measured

duplication rate pct 93.17 measured

How this grade was computed

Weighted mean of 2 scored metric(s) → 67/100

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 96 measured ×1 100%

adapter content pct 18.08 measured ×0.5 0%

QC cost 42 s compute

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