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ERR003990
ENAProvenance — who produced it, who reused it
Linked to 0 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.
No linked papers found in the corpus yet.
Deep data QC
33/100 · FStandardized, field-standard QC computed by touching the data — every metric states how it was obtained · evidence: measured
Data type / assay
bulk-RNA-seq
Organism
Danio rerio
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)
gc sd
12.48
measured
checksum ok
yes
reported
total bases
409577716
reported
total reads
5534834
reported
n content pct
0.002
measured
pct q20 bases
90
measured
pct q30 bases
0
measured
pct reads q30
0
measured
sampled bases
37000000
measured
sampled reads
1000000
measured
gc content pct
45
measured
polyg tail pct
0
measured
read length sd
0
measured
quality dropoff
-4.7
measured
read length max
37
measured
read length min
37
measured
read length n50
37
measured
max base quality
31
measured
mean read length
37
measured
max n pct per pos
0.011
measured
mean base quality
26.8
measured
pct reads lt 100bp
100
measured
read length median
37
measured
adapter content pct
0.34
measured
median read quality
27.6
measured
duplication rate pct
12.45
measured
overrepresented top pct
0.44
measured
How this grade was computed
Weighted mean of 4 scored metric(s) → 33/100
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
0
measured
×1
0%
mean base quality
26.8
measured
×0.6
0%
adapter content pct
0.34
measured
×0.4
100%
duplication rate pct
12.45
measured
×0.4
100%
QC cost
37 s compute
measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0