Description

This track displays regions of the Zv10/danRer10 assembly for which no variation was observed in the genome sequences of the founders of the NHGRI-1 zebrafish line.

Display Conventions and Configuration

The black regions are invariant with respect to the Zv9/danRer7 reference assembly, while the white regions can indicate variation in at least one NHGRI-1 founder, the trimming flanking an insertion or deletion, or insufficient read depth to confidently call the region as invariant.

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 alignments of paired-end reads 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, and included in this track. When insertions or deletions were encountered, an additional 10 bp was removed from either side of the variant.

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 Zelin Chen.

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