Panel Information and Genotype data

Antenna panel

• • Sample list (powerpoint version, worksheet)

Genotype data (filtered).

• • Whole-genome sequencing, filtered dataset.

    • Includes SNPs and short indels.

    • 5,076,990, variants x 59 samples

  • A binary Plink dataset (BED/BIM/FAM) (5,076,990, variants x 59 samples) zipped :

    • AntennaPanel_Filtered_PlinkBinary.zip

  • The same dataset split by chromosome, text Plink format (ped/map), zip archives:

    • chr1

    • chr2

    • chr3

    • chr4

    • chr5

    • chr6

    • chr7

    • chr8

    • chr9

    • chr10

    • chr11

    • chr12

Reference Panel

Sample information

• • • MAGIC reference list

    • How the 325 lines were selected

    • Mapping of MAGIC genotype name to GBS taxa name (IR nnn to MIB-mmm)
      

Genotype data (GBS)

• • • GBS DATA (2allele HMP) (hapmap 2-allele format, filtered, imputed, for partners only)

    • GBS DATA in VCF format (same as above)

      • README for SNP dataset

    • GBS Data imputed to 5.2M SNPs using Rice Imputation Server in Plink format

    • Plink file (Binary)

Additional info

• • • Phenotyping data for DTF50 (Days to 50% flowering, LS Means), GWAS-ready

[ Analyses results (GWAS) -From prior studies, some analyses results (slides 75 - 96) broken link]

• Explore the datasets in an interactive NextJournal notebook:
  https://nextjournal.com/a/7Na9Yp7hi24YiB8eQpF1FJ?token=2ZcynWb5jgorUmJ9yNpS32

Co-analysis of the Reference, Antenna panel with 3K

• • upcoming

Pilot study on reference panel

Special list of accessions for pathology (Azucena, RC10,....)

Removed items: antenna panel photos (outdated link)