NHGRI-1 Variants Track Settings
 
NHGRI-1 Variants

Display mode:   

Haplotype sorting display

Enable Haplotype sorting display
Haplotype sorting order:
using middle variant in viewing window as anchor.
If this mode is selected and genotypes are phased or homozygous, then each genotype is split into two independent haplotypes. These local haplotypes are clustered by similarity around a central variant. Haplotypes are reordered for display using the clustering tree, which is drawn in the left label area. Local haplotype blocks can often be identified using this display.
To anchor the sorting to a particular variant, click on the variant in the genome browser, and then click on the 'Use this variant' button on the next page.
using the order in which samples appear in the underlying VCF file
Haplotype clustering tree leaf shape:
draw branches whose samples are all identical as <
draw branches whose samples are all identical as [
Allele coloring scheme:
reference alleles invisible, alternate alleles in black
reference alleles in blue, alternate alleles in red
first base of allele (A = red, C = blue, G = green, T = magenta)
Haplotype sorting display height:

Filters

Exclude variants with Quality/confidence score (QUAL) score less than
Minimum minor allele frequency (if INFO column includes AF or AC+AN):

VCF configuration help

View table schema

Description

This track displays the variants detected in the NHGRI-1 zebrafish line of assembily danRer10.

Display Conventions and Configuration

The variants are presented as a VCF file. When viewed in "full" mode, the browser displays the proportion of the variants observed in the two founders of the NHGRI-1 line. This information can also be obtained by clicking individual variants and opening the "Detailed genotypes" menu.

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 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 considered high confidence, and those that differed from the reference in at least one founder were marked as variants. Variants in which the reference base was an "N" were excluded from this track.

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