Description

This track displays the nonsense mutations detected in the NHGRI-1 zebrafish line.

Display Conventions and Configuration

The affected base is indicated by the position of the entry. The name field indicates the alternative allele, and the color indicates if the variant was determined to be homozygous (red) or heterozygous (blue) in the NHGRI-1 population.

Methods

The founding pair of the NHGRI-1 line were sequenced to a depth of ~50x each on the Illumina MiSeq. Variants were called from paired-end alignments using bam2mpg (Teer et al. 2010), which produced a most probable genotype (MPG) score for each nucleotide. Bases for which both founders matched the reference, had an MPG score of at least 10, sequence coverage of at least 20x, and a ratio of MPG score to coverage greater than 0.5 were labeled as invariant relative to the reference. Nonsense mutations were annotated using the 2012-10-16 version of ANNOVAR (Wang et al. 2010), selecting those labeled as "stop loss". Nonsense variants are reported here as homozygous only if they were called as homozygous in both NHGRI-1 founders.

Credits

These data were produced by the Developmental Genomics Section and the NIH Intramural Sequencing Center at the National Human Genome Research Institute. For questions, please email Shawn Burgess or Matthew LaFave.

References

LaFave MC, Varshney GK, Vemulapalli M, Mullikin JC, Burgess SM. A Defined Zebrafish Line for High-Throughput Genetics and Genomics: NHGRI-1. Genetics. 2014. PMID: 25009150

Teer JK, Bonnycastle LL, Chines PS, Hansen NF, Aoyama N, Swift AJ, Abaan HO, Albert TJ; NISC Comparative Sequencing Program, Margulies EH, Green ED, Collins FS, Mullikin JC, Biesecker LG. Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res. 2010 Oct;20(10):1420-31. PMID: 20810667; PMC: PMC2945191

Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010 Sep;38(16):e164. PMID: 20601685; PMC: PMC2938201