SRX180718

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

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

Oryza sativa Indica Group WGS via Illumina HiSeq 2000 with 338.8M reads at good quality (96.5% Q20, 93.5% Q30) spanning 68.4B bases over the large rice genome. Deep coverage enables SNP discovery, structural-variant detection, and sequence-assembly refinement for this major food crop. High-depth short-read WGS ideal for rice breeding, crop-genetics mapping, and comparative genomics across Oryza subspecies.

Data type / assay

WGS

Organism

Oryza sativa Indica 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 68447088748 reported

total reads 338846974 reported

n content pct 0.355 measured

pct q20 bases 96.5 measured

pct q30 bases 93.5 measured

gc content pct 44.9 measured

mean read length 101 measured

mean base quality 36.2 measured

adapter content pct 16.18 measured

duplication rate pct 1.97 measured

How this grade was computed

Weighted mean of 3 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.

pct q30 bases 93.5 measured ×1 100%

duplication rate pct 1.97 measured ×0.5 100%

adapter content pct 16.18 measured ×0.4 0%

QC cost 43 s compute

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