Biology Reference
In-Depth Information
A
80
nb_genes
60
0
20
40
60
80
100
40
20
0
4
5
log10 (scaffold length)
6
B
0
206,775
413,550
620,325
827,100
1,033,875
0
206,775
413,550
620,325
827,100
1,033,875
Gaps
XenBase_genes
C
0
206,775
413,550
620,325
827,100
1,033,875
227,224
247,365
267,506
287,648
307,789
327,930
Gaps
XenBase_genes
Figure 10.1 The
genome assembly 4.1 is highly fragmented. (A) Scatterplot
representing the size of each scaffold (in log
10
scale) compared to the proportion of
assembly gaps (% Unsequenced). The gene number per scaffold (ranging from 0 to
100) is indicated by gray circles of various sizes. The three ellipses in the upper half
of the plot correspond to a fraction of the cosmid, fosmid, and BAC-end libraries used
to help the assembly process. The gene rich and almost fully sequenced scaffolds
capturing80% of the assembly are indicated at the bottom-right of the plot
(dashed-circle). (B) Illustrative example of the assembly gaps found in a scaffold. The
first track shows the assembly gaps (stretches of 'N's). The second track represents
XenBase gene models. The orientation of each gene is indicated by the direction of
the arrow. The scaffold shown is scaffold_448. (C) Close-up of a 100 kb region of
the scaffold_448. Assembly gaps that are exactly 50 bp long (“gaps of 50,” see text) are
indicated by arrows.
X. tropicalis
