The user can retrieve and export the whole dataset to an Excel file by opting one pseudo-molecule at a time (Ca1..Ca8), on the basic search page. The length of each chromosome is provided below:
| Chromosome | Length |
| Ca1 | 48,359,943 |
| Ca2 | 36,634,854 |
| Ca3 | 39,989,001 |
| Ca4 | 49,191,682 |
| Ca5 | 48,169,137 |
| Ca6 | 59,463,898 |
| Ca7 | 48,961,560 |
| Ca8 | 16,477,302 |
The SNPs from the search page have been linked to the JBrowse displaying the SNP information. For each of the variations a SNP ID has been assigned and by clicking on respective SNP IDs will redirect the user to a detailed information related to the variation on the JBrowse page.
Whether we can visualize other than these 90 genotype alignment files?
Yes, JBrowse supports the upload of alignment files as tracks. User can upload a BAM file for genotype of interest generated by aligning the reads of the genotype to chickpea reference genome (CDC Frontier, Varshney et al, 2013).
Can we upload and visualize other than BAM files?
JBrowse takes input of BED, BigWig, wiggle and VCF files as visualization tracks. For information, please refer “http://gmod.org/wiki/JBrowse_Configuration_Guide”.
What was the reason behind the usage of BAM files in CicArVarDB?
JBrowse supports different track types for displaying alignment data, particularly BAM files. We have provided the alignment file for the visualization of the variations via JBrowse, which perform a proof reading for the presence of a variant. User can visualize and analyze the variation on the basis of read depth, base quality and reads matching to altered base for each genotype.
Any advantage in the use of advanced search over basic search?
The advanced search method provides the user with more comprehensive selection criteria to choose at least any two of the listed options: Genomic location, SNP classification, SNP type and Selecting multiple genotypes, whereas basic search restricts the user to select only one option for a search. The results of both basic and advanced searches includes a table of genomic co-ordinates, bases present at the SNP position in reference genome sequence and corresponding variant base call.
Why BLAST is restricted to BLASTn in the CicArVarDB?
BLASTN search is integrated to find homologous region in the chickpea genome for the user given query sequence and the co-ordinates for resulting HSPs are used to identify the number of SNPs present in the region. The result page displays the SNP information along with its presence in the gene and associated gene annotation.
Why JBrowse?
JBrowse enables the users to upload BAM files as tracks to visualize alignment files faster as compared to other genome browsers.
Explain about the rationale of the “Multiple Genotypes” option in Advanced search? How it is useful to the user?
Multiple genotypes option in the advanced search results into variants observed in those genotypes with respect to a reference genome. Basic search provides an option of retrieving the variations between two genotypes. User can extract the variations in the genotype belonging to the same group.