SRX7828345

SRA first seen 2020

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

73/100 · C

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

What this means

claude:haiku

WGS short-read data (Senna tora). Grade C reflects critical adapter contamination at 22.79%, which will inflate error rates and degrade variant call accuracy. While base quality metrics are acceptable (Q30 87.7%), the uncontrolled adapter content is the primary liability for reuse; recommend adapter trimming verification before downstream work.

Data type / assay

WGS

Organism

Senna tora

Instrument

Illumina HiSeq 2500

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 19228113360 reported

total reads 95188680 reported

n content pct 0.007 measured

pct q20 bases 94.5 measured

pct q30 bases 87.7 measured

gc content pct 38.3 measured

mean read length 101 measured

mean base quality 34.6 measured

adapter content pct 22.79 measured

duplication rate pct 4.24 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 73/100

The C 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.

pct q30 bases 87.7 measured ×1 89%

duplication rate pct 4.24 measured ×0.5 100%

adapter content pct 22.79 measured ×0.4 0%

QC cost 21 s compute

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