Genetic Sample Data

Raw paired-end sequencing reads generated on Complete Genomics instrumentation.

• complete_R1.fastq.gz

  Forward (read 1) raw sequencing reads with per-base quality scores. (31.5 GB)

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• complete_R2.fastq.gz

  Reverse (read 2) mate reads pairing with the R1 file. (36.3 GB)

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Raw paired-end sequencing reads generated on Illumina instrumentation.

• illumina_R1.fastq.gz

  Forward (read 1) raw sequencing reads with per-base quality scores. (39.2 GB)

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• illumina_R2.fastq.gz

  Reverse (read 2) mate reads pairing with the R1 file. (40.1 GB)

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Called and annotated variants from an Illumina sequencing run.

• illumina_sv.vcf.gz

  Structural variant calls — large insertions, deletions, inversions and translocations. (3.8 MB)

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• illumina_cnv_sv.vcf.gz

  Combined copy-number and structural variant calls in a single VCF. (233 KB)

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• illumina_cnv.vcf.gz

  Copy-number variant calls with segment-level gain and loss states. (118 KB)

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• illumina_hard-filtered.vcf.gz

  Small-variant calls with low-confidence records removed by hard quality filters. (415 MB)

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• illumina_ploidy.vcf.gz

  Estimated ploidy and sex-chromosome karyotype calls per chromosome. (1.5 KB)

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Called and annotated variants from a Complete Genomics sequencing run.

• complete_sv.vcf.gz

  Structural variant calls — large insertions, deletions, inversions and translocations. (18 MB)

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• complete_cnv_sv.vcf.gz

  Combined copy-number and structural variant calls in a single VCF. (683 KB)

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• complete_cnv.vcf.gz

  Copy-number variant calls with segment-level gain and loss states. (75.8 KB)

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• complete_hard-filtered.vcf.gz

  Small-variant calls with low-confidence records removed by hard quality filters. (442 MB)

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• complete_mrjd.vcf.gz

  Machine-learned recalibrated joint detection calls for improved low-frequency sensitivity. (79.6 KB)

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• complete_mrjd_hard-filtered.vcf.gz

  The MRJD call set after hard filtering, retaining only high-confidence variants. (80.4 KB)

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• complete_cyto.vcf.gz

  Cytogenetics-style output summarising chromosome-scale events in ISCN-like terms. (45.3 KB)

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• complete_ploidy.vcf.gz

  Estimated ploidy and sex-chromosome karyotype calls per chromosome. (1.8 KB)

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• complete_repeats.vcf.gz

  Short tandem repeat expansion genotypes at known repeat loci. (6.9 MB)

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Infinium Global Screening Array v3 genotype calls for microarray-based variant testing.

• gsa_v3.txt

  Tab-delimited genotype calls for each array probe, with sample and marker IDs. (25.4 MB)

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Pharmacogenomic results describing drug-gene interactions and metaboliser phenotypes.

• complete_pgx.hl7

  HL7 clinical message containing pharmacogenomic star-allele calls and phenotype interpretations. (3.3 KB)

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