SRX7828349

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

66/100 · D

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

What this means

claude:haiku

WGS short-read data (Senna tora), grade D driven by severe 31.63% adapter contamination (scored 0/100), indicating incomplete adapter trimming or sample contamination. Secondary issue is borderline Q30 of 85.6%. Adapter content will degrade mapping specificity and inflate false variants; recommend pre-trimming quality audit before reuse.

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 45809819166 reported

total reads 226781283 reported

n content pct 0.004 measured

pct q20 bases 91.9 measured

pct q30 bases 85.6 measured

gc content pct 40.6 measured

mean read length 101 measured

mean base quality 33.8 measured

adapter content pct 31.63 measured

duplication rate pct 9.65 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 66/100

The D 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 85.6 measured ×1 78%

duplication rate pct 9.65 measured ×0.5 95%

adapter content pct 31.63 measured ×0.4 0%

QC cost 21 s compute

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