SRR039506

SRA first seen 2014

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

35/100 · F

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

What this means

claude:haiku

Short-read bulk RNA-seq from maize (Zea mays). Grade F; substandard Q30 (69.9%) and mean base quality 29.4 fail expression-seq thresholds. Short reads (35 bp) and moderate duplication (40.26%) on Genome Analyzer II compound the issue. Reuse only with aggressive quality filtering and acceptance of reduced sensitivity in downstream analysis.

Data type / assay

bulk-RNA-seq

Organism

Zea mays subsp. mays

Instrument

Illumina Genome Analyzer

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 463765190 reported

total reads 13250434 reported

n content pct 0.067 measured

pct q20 bases 92.7 measured

pct q30 bases 69.9 measured

gc content pct 56.2 measured

mean read length 35 measured

mean base quality 29.4 measured

adapter content pct 0.06 measured

duplication rate pct 40.26 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 35/100

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

pct q30 bases 69.9 measured ×1 0%

mean base quality 29.4 measured ×0.6 23%

adapter content pct 0.06 measured ×0.4 100%

duplication rate pct 40.26 measured ×0.4 77%

QC cost 33 s compute

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