SRX5136389

SRA first seen 2019

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

79/100 · C

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

What this means

claude:haiku

Short-read WGS, cattle. Grade C; extrapolated coverage (18.7×, scored 49/100) is insufficient for reliable variant calling—the critical limiting factor. Measured base quality is good; marginal for reuse without verified shallow-depth constraints or depth confirmation.

Data type / assay

WGS

Organism

Bos taurus

Instrument

Illumina HiSeq 4000

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 50461957046 reported

total reads 167092573 reported

mean coverage 18.7 extrapolated

n content pct 0.004 measured

pct q20 bases 96.3 measured

pct q30 bases 90.8 measured

gc content pct 43.9 measured

mean read length 151 measured

mean base quality 37.9 measured

adapter content pct 0.1 measured

duplication rate pct 10.27 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 79/100

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.

mean coverage 18.7 extrapolated ×1.2 49%

pct q30 bases 90.8 measured ×1 100%

duplication rate pct 10.27 measured ×0.5 93%

adapter content pct 0.1 measured ×0.4 100%

QC cost 47 s compute

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