SRX335472

ENA 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

63/100 · D

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

What this means

claude:haiku

Callithrix jacchus marmoset bulk RNA-seq Grade D catastrophically compromised by 81.26% adapter contamination (scored 0/100) plus moderate base quality (81.1% Q30). Unsuitable for expression analysis; aggressive trimming and resequencing are mandatory.

Data type / assay

bulk-RNA-seq

Organism

Callithrix jacchus

Instrument

Illumina MiSeq

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 10542051204 reported

total reads 21000102 reported

n content pct 0.008 measured

pct q20 bases 86 measured

pct q30 bases 81.1 measured

gc content pct 46.9 measured

mean read length 251 measured

mean base quality 33.6 measured

adapter content pct 81.26 measured

duplication rate pct 14.75 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 63/100

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 81.1 measured ×1 56%

mean base quality 33.6 measured ×0.6 93%

adapter content pct 81.26 measured ×0.4 0%

duplication rate pct 14.75 measured ×0.4 100%

QC cost 52 s compute

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