Table 3 |
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|
Pooled BAC assembly scores for five genomes |
||||||||
|
Species |
Pool Size |
Match |
Relocation |
Inversion |
Redundancy |
Coverage |
Scaffold N50 |
Number of scaffolds |
|
|
||||||||
|
A. thaliana |
3M |
0.527 |
0.994 |
0.954 |
0.962 |
87.44% |
117,128 |
57 |
|
A. thaliana |
6M |
0.518 |
0.997 |
0.976 |
0.969 |
86.55% |
126,619 |
100 |
|
A. thaliana |
9M |
0.511 |
0.927 |
0.985 |
0.975 |
85.72% |
121,006 |
144 |
|
A. thaliana |
12M |
0.510 |
0.999 |
0.981 |
0.982 |
87.36% |
147,618 |
152 |
|
V. vinifera |
3M |
0.524 |
0.997 |
0.955 |
0.988 |
84.76% |
114,280 |
60 |
|
V. vinifera |
6M |
0.511 |
0.997 |
0.974 |
0.972 |
80.60% |
113,117 |
143 |
|
V. vinifera |
9M |
0.510 |
0.997 |
0.953 |
0.969 |
82.96% |
116,543 |
173 |
|
V. vinifera |
12M |
0.507 |
0.994 |
0.941 |
0.973 |
82.48% |
115,403 |
226 |
|
O. sativa |
3M |
0.535 |
0.996 |
0.966 |
0.989 |
88.45% |
112,776 |
39 |
|
O. sativa |
6M |
0.519 |
0.983 |
0.895 |
0.983 |
87.10% |
140,891 |
90 |
|
O. sativa |
9M |
0.508 |
0.961 |
0.902 |
0.977 |
84.91% |
117,728 |
141 |
|
O. sativa |
12M |
0.507 |
0.958 |
0.869 |
0.979 |
84.72% |
114,523 |
219 |
|
P. trichocarpa |
3M |
0.529 |
1.000 |
0.984 |
0.981 |
82.68% |
134,082 |
65 |
|
P. trichocarpa |
6M |
0.513 |
1.000 |
0.980 |
0.992 |
82.31% |
119,756 |
114 |
|
P. trichocarpa |
9M |
0.508 |
1.000 |
0.995 |
0.992 |
81.39% |
124,798 |
182 |
|
P. trichocarpa |
12M |
0.506 |
1.000 |
0.979 |
0.989 |
80.99% |
117,268 |
256 |
|
S. bicolor |
3M |
0.542 |
0.945 |
0.944 |
0.957 |
86.56% |
148,894 |
37 |
|
S. bicolor |
6M |
0.520 |
0.889 |
0.939 |
0.955 |
86.03% |
147,854 |
81 |
|
S. bicolor |
9M |
0.508 |
0.922 |
0.898 |
0.953 |
84.59% |
112,136 |
213 |
|
S. bicolor |
12M |
0.504 |
0.905 |
0.859 |
0.953 |
83.57% |
96,480 |
274 |
|
Z. mays |
3M |
0.506 |
0.872 |
0.734 |
0.835 |
76.38% |
52,719 |
140 |
|
Z. mays |
6M |
0.503 |
0.857 |
0.679 |
0.832 |
79.31% |
40,526 |
320 |
|
Z. mays |
9M |
0.502 |
0.847 |
0.687 |
0.820 |
80.33% |
37,394 |
485 |
|
Z. mays |
12M |
0.501 |
0.855 |
0.674 |
0.815 |
82.39% |
37,122 |
577 |
|
|
||||||||
|
Evaluation scores and scaffold statistics for assemblies determined using 15x linear + 5x paired read coverage and pool sizes 3 Mbp, 6 Mbp, 9 Mbp, and 12 Mbp are shown for all of the genomes studied. Default assembly parameters were used. |
||||||||
|
Haiminen et al. BMC Genomics 2011 12:194 doi:10.1186/1471-2164-12-194 |
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