PRJNA649355

BioProject first seen 2020

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

21/100 · F

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

What this means

claude:haiku

This HIV-1 WGS from Ion Torrent Proton totals 1.73 billion bases with low quality (4.7% Q30), consistent with Ion Torrent limitations. Despite poor base quality, the dataset enables assessment of viral genome variation.

Data type / assay

WGS

Organism

Human immunodeficiency virus 1

Instrument

Ion Torrent Proton

Platform

ION_TORRENT

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

3 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 1727395654 reported

total reads 10434239 reported

n content pct 0 measured

pct q20 bases 87.9 measured

pct q30 bases 4.7 measured

gc content pct 49.5 measured

mean read length 166.5 measured

mean base quality 24.5 measured

adapter content pct 0 measured

duplication rate pct 83.08 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 21/100

The F grade is a transparent weighted average. Each metric below scored from 0–100% against the published WGS thresholds, weighted by its importance; nothing is hidden or subjective.

pct q30 bases 4.7 measured ×1 0%

duplication rate pct 83.08 measured ×0.5 0%

adapter content pct 0 measured ×0.4 100%

QC cost 24 s compute

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