PRJEB11828

BioProject first seen 2016

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

100/100 · A

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

What this means

claude:haiku

Neanderthal WGS representing exceptional sequencing quality with near-perfect Q30 (98.9%), vanishingly low duplication (0.61%), and high base quality (58.4), likely reflecting meticulous ancient-DNA library preparation; excellent foundation for archaic human population genetics.

Data type / assay

WGS

Organism

Homo sapiens neanderthalensis

Instrument

Illumina Genome Analyzer IIx

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads), BAM/CRAM (aligned)

N numbers (samples, groups)

116 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 4278818084 reported

total reads 65734716 reported

n content pct 0.005 measured

pct q20 bases 99.5 measured

pct q30 bases 98.9 measured

gc content pct 38.2 measured

mean read length 65.1 measured

mean base quality 58.4 measured

adapter content pct 0 measured

duplication rate pct 0.61 measured

How this grade was computed

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

The A 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 98.9 measured ×1 100%

duplication rate pct 0.61 measured ×0.5 100%

adapter content pct 0 measured ×0.4 100%

QC cost 22 s compute

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