Potato-Utricularia-Genlisea Syntenic Depth: Difference between revisions

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[[Syntenic depth]] measurements permit classifying the number of whole genome duplications that have happened in one lineage relative to another. Unfortunately, these analyses are not 100% conclusive, but provide supporting evidence, especially when combined with [[Syntenic dotplots]].  
[[Syntenic depth]] measurements permit classifying the number of whole genome duplications that have happened in one lineage relative to another. Unfortunately, these analyses are not 100% conclusive, but provide supporting evidence, especially when combined with [[Syntenic dotplots]].  


Table of syntenic depth measurements of potato versus Utricularia and Genlisea:<br>
==4 genes in 80==
Syntenic Depth: http://genomevolution.org/r/4rl2


{| cellspacing="1" cellpadding="1" border="1" style="width: 503px; height: 498px;"
Genlisea aurea
|-
<pre>Depth 1 2056 of 2820 72.91%
| Parameters<br>  
Depth 2 405 of 2820 14.36%
| Results<br>
Depth 3 346 of 2820 12.27%
|-
Depth 4 8 of 2820 0.28%
|
Depth 5 5 of 2820 0.18%</pre>
Window size: 10  
Utricularia gibba
<pre>Depth 1 11526 of 27145 42.46%
Depth 2 6849 of 27145 25.23%
Depth 3 4346 of 27145 16.01%
Depth 4 2456 of 27145 9.05%
Depth 5 1254 of 27145 4.62%
Depth 6 534 of 27145 1.97%
Depth 7 138 of 27145 0.51%
Depth 8 28 of 27145 0.10%
Depth 9 8 of 27145 0.03%
Depth 10 4 of 27145 0.01%
Depth 12 1 of 27145 0.00%
Depth 13 1 of 27145 0.00%</pre>


Cutoff: 0.1%<br>
[[Potato-Utricular-Genlisea Syntenic Depth old data]]
 
(One syntenic genes in a span of 10 genes)<br>
 
http://genomevolution.org/r/4nfz<br>
 
|
'''Genlisea aurea'''<br>Depth 1 5196 of 5705 91.08%<br>Depth 2 446 of 5705 7.82%<br>Depth 3 58 of 5705 1.02%<br>Depth 4 5 of 5705 0.09%<br>
 
<br>'''Utricularia gibba'''<br>Depth 1 9307 of 14433 64.48%<br>Depth 2 3393 of 14433 23.51%<br>Depth 3 1130 of 14433 7.83%<br>Depth 4 382 of 14433 2.65%<br>Depth 5 134 of 14433 0.93%<br>Depth 6 51 of 14433 0.35%<br>Depth 7 26 of 14433 0.18%<br>Depth 8 6 of 14433 0.04%<br>Depth 9 4 of 14433 0.03%
 
|-
| Window size: 10
Cutoff: 0.2%
 
(Two syntenic genes in a span of 10 genes)<br>
 
http://genomevolution.org/r/4nlz<br>
 
|
'''Genlisea aurea'''<br>Depth 1 1436 of 1478 97.16%<br>Depth 2 39 of 1478 2.64%<br>Depth 3 3 of 1478 0.20%<br>
 
<br>'''Utricularia gibba'''<br>Depth 1 3384 of 4215 80.28%<br>Depth 2 651 of 4215 15.44%<br>Depth 3 124 of 4215 2.94%<br>Depth 4 42 of 4215 1.00%<br>Depth 5 9 of 4215 0.21%<br>Depth 6 5 of 4215 0.12%<br>
 
|-
| Window size: 5
Cutoff: 0.1%
 
(One syntenic genes in a span of 5 genes)
 
http://genomevolution.org/r/4nlx<br>
 
|
'''Genlisea aurea'''<br>Depth 1 1295 of 1316 98.40%<br>Depth 2 21 of 1316 1.60%
 
<br>'''Utricularia gibba'''<br>Depth 1 2631 of 3158 83.31%<br>Depth 2 460 of 3158 14.57%<br>Depth 3 59 of 3158 1.87%<br>Depth 4 6 of 3158 0.19%<br>Depth 5 2 of 3158 0.06%<br>
 
|-
| Window size: 20<br>
Cutoff: 0.1%
 
(two syntenic genes in a span of 20 genes)
 
http://genomevolution.org/r/4nm1<br>
 
| '''Genlisea aurea'''<br>Depth 1 2732 of 2880 94.86%<br>Depth 2 142 of 2880 4.93%<br>Depth 3 6 of 2880 0.21%
'''Utricularia gibba'''<br>Depth 1 7097 of 9850 72.05%<br>Depth 2 1919 of 9850 19.48%<br>Depth 3 569 of 9850 5.78%<br>Depth 4 171 of 9850 1.74%<br>Depth 5 59 of 9850 0.60%<br>Depth 6 20 of 9850 0.20%<br>Depth 7 6 of 9850 0.06%<br>Depth 8 4 of 9850 0.04%<br>Depth 9 2 of 9850 0.02%<br>Depth 10 1 of 9850 0.01%<br>Depth 12 1 of 9850 0.01%<br>Depth 13 1 of 9850 0.01%<br><br>
 
|}
 
<br>

Latest revision as of 18:41, 4 May 2012

Follow this link for information on Syntenic depth.

Syntenic depth measurements permit classifying the number of whole genome duplications that have happened in one lineage relative to another. Unfortunately, these analyses are not 100% conclusive, but provide supporting evidence, especially when combined with Syntenic dotplots.

4 genes in 80

Syntenic Depth: http://genomevolution.org/r/4rl2

Genlisea aurea 

Depth 1	2056	of	2820	72.91%
Depth 2	405	of	2820	14.36%
Depth 3	346	of	2820	12.27%
Depth 4	8	of	2820	0.28%
Depth 5	5	of	2820	0.18%

Utricularia gibba 

Depth 1	11526	of	27145	42.46%
Depth 2	6849	of	27145	25.23%
Depth 3	4346	of	27145	16.01%
Depth 4	2456	of	27145	9.05%
Depth 5	1254	of	27145	4.62%
Depth 6	534	of	27145	1.97%
Depth 7	138	of	27145	0.51%
Depth 8	28	of	27145	0.10%
Depth 9	8	of	27145	0.03%
Depth 10	4	of	27145	0.01%
Depth 12	1	of	27145	0.00%
Depth 13	1	of	27145	0.00%

Potato-Utricular-Genlisea Syntenic Depth old data

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