Interacting with displayed items in SVA genome browser - identified variants

 

You can interact (by mousing clicking or keyboard) with most of the items displayed in the SVA genome browser to obtain detailed information or to navigate to public databases. In this page again I am going to use the example project released with SVA to show how to do this.

As a reminder, every section in black background comes from data generated by you, and other sections in yellow background come from public databases. This page will focus on identified variants from your project.

1. Identified Single Nucleotide Variants (SNVs)

Below is a typical section plotting the identified SNVs. Both the blue drop down button on the left , and each of the individual green SNV line on the black background are clickable.

1.1 Clicking on the button will bring up a popup menu summarizing the SNVs in this section (figure below). This small popup menu firstly provides a very brief summary on the region and how many SNPs are plotted, then offers a function to list the detailed information for these SNVs.

Clicking on the "List all identified SNVs" will bring up a SNV table like this:

From left to right, the columns displayed are:

SNP serial number , number of subjects carrying this variant (click for more infomation) , chromosome, position, alternative allele, reference allele, strand (illumina top/bottom definition) , Phred-like consensus score (average across subjects), SNP quality (average across subjects), RMS score (average across subjects), read depth (average across subjects), function for the SNV, the corresponding transcript for the function * , the KEGG pathway for the gene, gene ontology term for the gene, exisiting rs# if any, if in HapMap database, if in Illumina Infinium HD Human1M BeadChip, if in Dr. Venter's sequence, if in any control genome.

* note one variant may have more than category of functions, and/or a same function for several transcripts belonging to a same gene or several different genes.

In the example showed above, we noticed a "stop_gained" SNV in the Factor VIII (F8) gene. Clicking on this function will bring up a small information box showing where the variant occurs and whether it is tolerable and the tolerance P value (for non-synonymous SNVs).

Further clicking on column 2 (number of subjects carrying this variant) will bring up this subject information table:

From left to right, the columns displayed are:

SNP serial number , subject ID, genotype, reference allele, strand (illumina top/bottom definition) , Phred-like consensus score ( subject-specific), SNP quality (subject-specific), RMS score (subject-specific), read depth (subject-specific), how many reads supporting the alternative allele, how many reads supporting the reference allele, exisiting rs# if any.

As you can see from this table, the evidence supporting that subject hemo0022 carries this X chromosome premature stop SNP is strong: the SNV quality is 63, and all 12 reads support the alternative allele, and none of the reads support the reference allele.

1.2 Clicking on the individual SNV green line will bring up a SNV table like this:

This table shows similar information with the multiple SNV table above, but only restricted to the SNV you clicked. Please note you may use the left (<) and right (>) button to move to previous or next SNV plotted in the section. This function is very useful particularly when the SNV density is high so it is difficult to directly click on the right one.

Lastly, please note that the section "Identified SNVs with an rs number" displays the similar information but restricted to all rs# available SNVs. Interacting with that section is identical to this section.

2. Identified Insertion/Deletions (INDELs) \

Similarly, both the blue drop down button on the left , and each of the individual green INDEL line on the black background are clickable.

2.1 Clicking on the button and then on "List all small indels" will bring up an INDEL table like this:

From left to right, the columns displayed are:

INDEL serial number , number of subjects carrying this variant (click for more infomation) , chromosome, type (insertion or deletion), start position, end position, length of variant, bases inserted or deleted, INDEL quality (average across subjects), read depth (average across subjects), number of reads supporting INDEL (average across subjects), function for the INDEL, the corresponding transcript for the function, the KEGG pathway for the gene, gene ontology term for the gene, related dbSNP entry, related variant in Dr. Venter's sequence, if in control genomes.

it is interesting to see that in addition to 4 "coding disrupting frameshifting" INDELs observed only in cases, there is one occuring in one of the control genomes (indicated 'yes' in control genome). Detailed inspection indicates that out of total 15 reads covering this site, there are 9 supporting reference sequence, 2 supporting the INDEL, and 4 supporting other alleles. We then concluded this reported INDEL is actually a sequencing mistake.

Further clicking on column 2 (number of subjects carrying this variant) will bring up this subject information table:

From left to right, the columns displayed are:

INDEL serial number , type (ins or del), chromosome, start, end, bases inserted or deleted, related dbSNP entry, related variant in Dr. Venter's sequence, subject ID, homozygous status, INDEL quality (subject-specific), Phred-like consensus score ( subject-specific), total read depth (subject-specific), how many reads supporting the INDEL, how many reads supporting the reference allele.

As you can see from this table, the evidence supporting that subject hemo0017 carries this X chromosome "coding disrupting frameshifting" INDEL is strong: the INDEL quality is 501, and out of 15, 12 reads support the INDEL, and none of the reads support the reference allele.

2.2 Clicking on the individual INDEL green line will bring up a INDEL table like this:

This table shows similar information with the multiple INDEL table above, but only restricted to the INDEL you clicked. Again please note you may use the left (<) and right (>) button to move to previous or next INDEL plotted in the section.

Hint You can introduce the identified coding INDELs or missense SNVs into known gene coding sequences, so that you can see what coding change they can result in. This is detailed here.