Additional data file 1.

Supplemental Table 1: result of the NGS pipeline analysis. Supplemental Table 2: coverage information of all the samples in each NGS. Supplemental Table 3: coverage variability between amplicons. Supplemental Table 4: coverage variability between different repeat elements. Supplemental Table 5: amount of sequence with no or low coverage. Supplemental Table 6: list of regions with no or low coverage for each NGS. Supplemental Table 7: analysis of the allelic imbalance amplification of the LR-PCR amplicons. Supplemental Table 8: result of the comparison between sequencing and genotyping on Illumina Hap550. Supplemental Table 9: loci with discrepant calls between genotyping and sequencing. Supplemental Table 10: genotype calls comparison between ABI Sanger and each NGS. Supplemental Table 11: quality metrics of the comparison of the genotype calls between ABI Sanger and NGS technologies. Supplemental Table 12: all the loci with discordant genotype calls between ABI Sanger and NGS Technologies. Supplemental Table 13: all indel loci identified by ABI Sanger and their calls in Roche 454. Supplemental Table 14: all indels identified by Roche 454 and missed by ABI Sanger. Supplemental Table 15: all the primers and oligonucleotides used in the study.

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Harismendy et al. Genome Biology 2009 10:R32   doi:10.1186/gb-2009-10-3-r32