Variants in lacO Mutants (Filtered) Track Settings
 
Genetic Variations in lacO Mutants (Filtered)   (All Variations tracks)

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
Exclude variants with these FILTER values:
 
PASS (All filters passed)
FS_gt_200 (FS > 200.0)
FS_gt_60 (FS > 60.0)
LowQual (Low quality)
MQRS_lt_n12.5 (MQRankSum < -12.5)
MQ_lt_40 (MQ < 40.0)
QD_lt_2 (QD < 2.0)
QUAL_lt_30 (QUAL < 30.0)
RPRS_lt_n20 (ReadPosRankSum < -20.0)
RPRS_lt_n8 (ReadPosRankSum < -8.0)
SOR_gt_3 (SOR > 3.0)
Minimum minor allele frequency (if INFO column includes AF or AC+AN):

VCF configuration help

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Data last updated at UCSC: 2022-10-21

Description

This track shows the sequence variants in the D. melanogaster lacO mutants that cause changes in the transcribed exons (e.g., UTR variants, missense variants, frame shifts). Variants found in the control samples were excluded from this evidence track.

The sequence variants were identified by GATK 4. The effect of the variants were predicted by the Ensembl Variant Effect Predictor (VEP).

References

McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. The Ensembl Variant Effect Predictor. Genome Biol. 2016 Jun 6;17(1):122.

Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43:11.10.1-11.10.33.