SRP056824

ENA first seen 2015

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

62/100 · D

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

What this means

claude:haiku

Sugarcane bulk RNA sequencing with below-standard base quality. Poor QC (62/100, D) with Q30 of 77.7% and mean base quality of 31.1, both falling below acceptable thresholds for quantifying lowly-expressed transcripts; these deficiencies will introduce errors in gene expression estimates. Not recommended for high-confidence expression profiling.

Data type / assay

bulk-RNA-seq

Organism

Saccharum hybrid cultivar

Instrument

Illumina HiSeq 2000

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 2796639000 reported

total reads 27966390 reported

n content pct 0.023 measured

pct q20 bases 84.5 measured

pct q30 bases 77.7 measured

gc content pct 53.5 measured

mean read length 100 measured

mean base quality 31.1 measured

adapter content pct 0.54 measured

duplication rate pct 10.53 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 62/100

The D 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 77.7 measured ×1 39%

mean base quality 31.1 measured ×0.6 52%

adapter content pct 0.54 measured ×0.4 100%

duplication rate pct 10.53 measured ×0.4 100%

QC cost 34 s compute

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