SRX180537

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

83/100 · B

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

What this means

claude:haiku

Large-scale whole-genome sequencing of Oryza sativa Indica Group (rice) on Illumina HiSeq 2000 with 412.3 million reads and good quality (95.5% Q20, 91.8% Q30) provides comprehensive variant detection in this staple crop. The substantial dataset enables population-level crop genomics, breeding-marker identification, and agronomic-trait association studies.

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 83285580710 reported

total reads 412304855 reported

n content pct 0.152 measured

pct q20 bases 95.5 measured

pct q30 bases 91.8 measured

gc content pct 44.1 measured

mean read length 101 measured

mean base quality 35.7 measured

adapter content pct 12.43 measured

duplication rate pct 1.77 measured

How this grade was computed

Weighted mean of 3 scored metric(s) → 83/100

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 91.8 measured ×1 100%

duplication rate pct 1.77 measured ×0.5 100%

adapter content pct 12.43 measured ×0.4 18%

QC cost 1 min compute

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