SRR12833630

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 amplicon short-read sequencing, grade D (not recommended without processing). Adapter contamination at 15.57% dominates the assessment despite solid base quality (Q30 94.2%); adapter trimming is necessary before downstream variant analysis.

Data type / assay

amplicon

Organism

Severe acute respiratory syndrome coronavirus 2

Instrument

NextSeq 550

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 408831244 reported

total reads 1400107 reported

n content pct 0.006 measured

pct q20 bases 96.3 measured

pct q30 bases 94.2 measured

gc content pct 38.6 measured

mean read length 146 measured

mean base quality 34.6 measured

adapter content pct 15.57 measured

duplication rate pct 89.12 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 94.2 measured ×1 100%

adapter content pct 15.57 measured ×0.5 0%

QC cost 23 s compute

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