Table 3.
Comparison between Douglas-fir isotigs and white spruce unigenes[16]
| Number of isotigs | |||||||
|---|---|---|---|---|---|---|---|
|
Class* |
No. of WS matches† |
Do other DF match the same WS?§ |
Do other matching DF overlap?‡ |
Isotig confidence# |
I1 subset (1 isotig per isogroup) (18,774) |
IM subset (>1 isotig per isogroup) (19,815) |
Example visual representations@ |
| C1 |
1 |
No |
- |
Highest |
5140 |
261 |
 |
| C2 |
2+ |
No |
- |
Higher |
896 |
88 |
 |
| C3 |
1 |
Yes |
No |
Higher |
1767 |
577 |
 |
| C4 |
2+ |
Yes |
No |
Medium |
586 |
159 |
 |
| C5 |
1 |
Yes |
Yes |
Lower |
1736 |
6974 |
 |
| C6 |
2+ |
Yes |
Yes |
Lowest |
3405 |
7040 |
 |
| |
Subtotal |
- |
- |
- |
13,530 |
15,099 |
|
| C7 | No matches | - | - | Unknown | 5244 | 4716 | |
*Douglas-fir (DF) isotigs were categorized into seven classes (C1-C7) and three levels of confidence based on their relationships to white spruce (WS) contigs using the SCARF program [68].
†Number of white spruce contigs that matched the Douglas-fir query.
§‘Yes’ indicates that at least one non-query isotig also matched the same white spruce contig.
‡‘Yes’ indicates that the query and at least one non-query isotig matched the same region of the white spruce contig (overlapped).
#Subjective level of confidence in the isotig assembly based on the information presented in columns 2–4.
@Cross-hatched bars represent white spruce contigs, black bars represent query Douglas-fir isotigs, and white bars represent non-query Douglas-fir isotigs.