Cluster no. 149

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Cluster is part of supercluster: 69

Cluster characteristics:

size 2082
size_real 2082
ecount 22431
supercluster 69
annotations_summary 5.81% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT
0.14% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT
0.14% Class_I/pararetrovirus:PARA-RT
0.10% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT
0.05% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RT
0.05% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-RT
pair_completeness 0.794827586206897
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.00048030739673391
satellite_probability 3.20953330666128e-23
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S8 2
S5 706
S4 689
S7 2
S9 7
S6 676
S2 0
S1 0
S3 0
comparative analysis - number of edges between species:
S8 S5 S4 S7 S9 S6 S2 S1 S3
S8 0.0 10.5 6.0 0.0 0.0 7 0 0 0
S5 10.5 2460.0 2420.0 12.0 26.0 2450 0 0 0
S4 6.0 2420.0 2450.0 3.0 16.5 2490 0 0 0
S7 0.0 12.0 3.0 0.0 0.5 6 0 0 0
S9 0.0 26.0 16.5 0.5 0.0 20 0 0 0
S6 7.0 2450.0 2490.0 6.0 20.0 2590 0 0 0
S2 0.0 0.0 0.0 0.0 0.0 0 0 0 0
S1 0.0 0.0 0.0 0.0 0.0 0 0 0 0
S3 0.0 0.0 0.0 0.0 0.0 0 0 0 0
comparative analysis - observed/expected number of edges between species
S8 S5 S4 S7 S9 S6 S2 S1 S3
S8 0.000 1.360 0.775 0.000 0.000 0.884 NA NA NA
S5 1.360 1.010 0.996 1.700 1.250 0.985 NA NA NA
S4 0.775 0.996 1.010 0.424 0.795 1.000 NA NA NA
S7 0.000 1.700 0.424 0.000 8.280 0.828 NA NA NA
S9 0.000 1.250 0.795 8.280 0.000 0.942 NA NA NA
S6 0.884 0.985 1.000 0.828 0.942 1.020 NA NA NA
S2 NA NA NA NA NA NA NA NA NA
S1 NA NA NA NA NA NA NA NA NA
S3 NA NA NA NA NA NA NA NA NA

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
pararetrovirus PARA-RT pararetrovirus PARA-RT 3 0.00144
CRM Ty3-RT CRM Ty3-RT 1 0.00048
Chlamyvir Ty3-RT Chlamyvir Ty3-RT 3 0.00144
Galadriel Ty3-RT Galadriel Ty3-RT 2 0.00096
Tcn1 Ty3-RT Tcn1 Ty3-RT 1 0.00048
Tekay Ty3-RT Tekay Ty3-RT 121 0.05812

clusters with similarity:

Cluster Number of similarity hits
86 63
95 31
142 1

clusters connected through mates:

Cluster Number of shared
read pairs		 k
86 57 0.0919
95 40 0.0601
3710 4 0.0327
142 3 0.00974
11300 3 0.0249
25 2 0.00229
84 2 0.00231
369 2 0.0127
664 2 0.0159
19800 2 0.0166
56400 2 0.0167
68700 2 0.0167
2 1 6e-04
3 1 0.00034
6 1 0.000362
15 1 0.000418
29 1 0.000864
35 1 0.000912
37 1 0.00116
67 1 0.00103
97 1 0.00335
207 1 0.00727
219 1 0.00699
240 1 0.0059
556 1 0.00775
1680 1 0.00797
8000 1 0.00826
9510 1 0.00826
9610 1 0.00826
10800 1 0.00833
18800 1 0.0083
70200 1 0.00833

CL149 ----> CL86

image

No. of shared pairs: :57

CL149 ----> CL95

image

No. of shared pairs: :40