The
Populus trichocarpa Genome Browser hosts
Populus
trichocarpa genome information and
Populus nigra sequence
data by using tracks classified in different sections.
Each section is exaplained below.
Linked tracks provide the corresponding source file in GFF3 format.
DNA-seq Illumina profiles |
Sequencing profiling using Illumina deep-sequencing.
Alignments were performed using FA2ST software.
P. nigra reads have been aligned against
P. trichocarpa genome reference sequence.
Two different alignments tracks are available for each
P. nigra individual:
- all alignments (plot of multiple hit counts,
random chosen, partitioned over hit positions);
- unique alignments.
Plots use a log 10 scale.
|
General |
The DNA/GC Content track represents the GC content in the genome.
The track scale is in %.
|
Genes |
Gene annotation based on P. trichocarpa v6.0 GFF3 file.
|
SNPs |
The SNP detection was performed by using CLC Genomics Workbench
3.7.1 software.
For each P. nigra individual two SNPs tracks are available:
- P. trichocarpa - P. nigra track
represents SNPs between the two species;
- P. nigra track represents SNPs within
P. nigra species.
Detailed view is limited to 500 kbp. For large regions
(500 - 50 kbp) a SNP distribution is shown by histograms.
Data scale varies between 0 and 80
For small regions (49 kbp - 1 bp) single SNPs are reported:
positioning the mouse pointer onto the SNP, a balloon will appear
showing the genotype. Clicking on it you will obtain exhaustive
information about it.
|
Kmers |
Genome (exact) 20-mers profile. They express the degree of
repetitiveness in the current window. Data is cut at height 10.
|
Analysis |
Restriction sites tracks show cut sites for the following
restriction enzymes:
|
Genome Browser
Our genome browser is available at
http://services.appliedgenomics.org/gbrowse/populus/. The access is
restricted to the partners involved in the joint European effort for
the high-throughput resequencing of Populus nigra genome.
