PRJNA764549

BioProject 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

68/100 · D

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

What this means

claude:haiku

Arabidopsis thaliana hybrid WGS via NovaSeq 6000 (platform listed as BGISEQ) from 12 samples totaling 390 billion bases with extremely high extrapolated coverage (2889.9x); however, Q20 rate drops dramatically to 21.4%, indicating severe quality degradation that severely limits variant calling reliability.

Data type / assay

WGS

Organism

Arabidopsis thaliana

Instrument

Illumina NovaSeq 6000

Platform

BGISEQ

Read type

hybrid (short+long)

Files available

FASTQ (raw reads)

N numbers (samples, groups)

12 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 390132151719 reported

total reads 919820449 reported

mean coverage 2889.9 extrapolated

n content pct 0 measured

pct q20 bases 21.4 measured

pct q30 bases 1 measured

gc content pct 36.5 measured

mean read length 23920.2 measured

mean base quality 13.2 measured

adapter content pct 0.04 measured

duplication rate pct 0.45 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 68/100

The D 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.

mean coverage 2889.9 extrapolated ×1.2 100%

pct q30 bases 1 measured ×1 0%

duplication rate pct 0.45 measured ×0.5 100%

adapter content pct 0.04 measured ×0.4 100%

QC cost 32 s compute

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