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1. • Add a Data Provider to IGB using the following URL: http://igbquickload.org/smokeTestingQuickload/
     
     •  The added Quickload site is available for the Homo sapien genome under the Available Data pane.
       
       
       
     • Verify that all files in the Quickload site are loading into IGB:
       
       • Bam
         •  Bam_HomoSapien.bam
           
       • Bed
         •  Bed_HomoSapien.bed
         •  Bed_HomoSapien.bed.gz
           
           
           
       • BedGraph
         •  BedGraph_HomoSapien.bedgraph
         •  BedGraph_HomoSapien.bedgraph.gz
           
       • BigBed
         •  BigBed_HomoSapien.bigbed
           
       • BigWig
         •  BigWig_HomoSapien,bigwig
           
       • GFF3
         •  GFF3_HomoSapien.gff3
         •  GFF3_HomoSapien.gff3.gz
       • GTF
         •  GTF_HomoSapien.gtf
         •  GTF_HomoSapien.gtf.gz
       • NarrowAndBroadPeak
         •  BroadPeak_HomoSapien.broadpeak
         •  BroadPeak_HomoSapien.broadpeak.gz
           
         •  NarrowPeak_HomoSapien.narrowpeak
         •  NarrowPeak_HomoSapien.narrowpeak.gz
           
       • VCF
         •  VCF_HomoSapien_Mutations(SNPs).vcf
         •  VCF_HomoSapien_Mutations(SNPs).vcf.gz
           •  Can you see mutations (SNPs)?
             
         •  VCF_HomoSapien_InsertionsAndDeletions.vcf
         •  VCF_HomoSapien_InsertionsAndDeletions.vcf.gz
           •  Can you see deletions?
             
           •  Can you see insertions?
             
       • Wig
         •  Wig_HomoSapien.wig
         •  Wig_HomoSapien.wig.gz

Sequence appearance

Go to the Arabidopsis genome.  From the RNA-Seq quicklaod (available by default as of 9.0.1), open the file RNA-Seq / Pollen SRP022162 / Reads / Pollen alignments.  (url http://lorainelab-quickload.scidas.org/rnaseq/A_thaliana_Jun_2009/SRP022162/Pollen.bam)

Go to location:   Chr1:7,319,301-7,319,375

Optimize the stack height, and compare the main view to this image:

Image Added

Verify that:

•  single base mismatches of A, T, C, and G appear with a color scheme that matches the sequence in the coordinate axis (the bottom).
•  deletions appear as shown, a gray space with a dash.
•  insertions appear as shown (see position 7,319,310 in image)

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