SRX734432

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

87/100 · B

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

What this means

claude:haiku

This whole-genome sequencing of rice (Oryza sativa Japonica) on Illumina HiSeq 2000 generated ~245 million short reads totaling 49.5 billion bases with exceptional quality (96.7% ≥Q20). The substantial depth and consistent per-base accuracy enable robust variant calling and genome assembly in this major crop species.

Data type / assay

WGS

Organism

Oryza sativa Japonica Group

Instrument

Illumina HiSeq 2000

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 49498124036 reported

total reads 245040218 reported

n content pct 0.024 measured

pct q20 bases 96.7 measured

pct q30 bases 91.7 measured

gc content pct 43.8 measured

mean read length 101 measured

mean base quality 35.8 measured

adapter content pct 9.67 measured

duplication rate pct 0.43 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 87/100

The B 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 91.7 measured ×1 100%

duplication rate pct 0.43 measured ×0.5 100%

adapter content pct 9.67 measured ×0.4 38%

QC cost 18 s compute

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