Cluster no. 63

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Cluster is part of supercluster: 1

Cluster characteristics:

size 4858
size_real 4858
ecount 203217
supercluster 1
annotations_summary 20.15% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT
12.39% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-GAG
5.23% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-PROT
2.00% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RT
1.03% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-GAG
1.03% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RT
0.66% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-PROT
0.51% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-PROT
0.49% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT
0.10% Class_I/pararetrovirus:PARA-RT
0.06% Class_I/LTR/Ty3_gypsy/chromovirus/Galadriel:Ty3-RT
0.04% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-unclass:Ty3-RT
0.02% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila:Ty3-RH
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-GAG
0.02% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-INT
pair_completeness 0.725754884547069
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.000617538081515027
satellite_probability 9.81425038973844e-23
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S8 3
S5 1660
S4 1600
S7 0
S9 0
S6 1590
S2 2
S1 0
S3 4
comparative analysis - number of edges between species:
S8 S5 S4 S7 S9 S6 S2 S1 S3
S8 0 22 18.0 0 0 18.0 0.0 0 0.0
S5 22 23100 23300.0 0 0 21900.0 41.0 0 51.0
S4 18 23300 23700.0 0 0 22300.0 33.5 0 59.0
S7 0 0 0.0 0 0 0.0 0.0 0 0.0
S9 0 0 0.0 0 0 0.0 0.0 0 0.0
S6 18 21900 22300.0 0 0 20700.0 26.5 0 58.5
S2 0 41 33.5 0 0 26.5 0.0 0 0.0
S1 0 0 0.0 0 0 0.0 0.0 0 0.0
S3 0 51 59.0 0 0 58.5 0.0 0 1.0
comparative analysis - observed/expected number of edges between species
S8 S5 S4 S7 S9 S6 S2 S1 S3
S8 0.000 1.130 0.908 NA NA 0.970 0.000 NA 0.000
S5 1.130 1.000 0.998 NA NA 1.000 1.210 NA 0.893
S4 0.908 0.998 0.999 NA NA 1.000 0.971 NA 1.020
S7 NA NA NA NA NA NA NA NA NA
S9 NA NA NA NA NA NA NA NA NA
S6 0.970 1.000 1.000 NA NA 0.997 0.820 NA 1.080
S2 0.000 1.210 0.971 NA NA 0.820 0.000 NA 0.000
S1 NA NA NA NA NA NA NA NA NA
S3 0.000 0.893 1.020 NA NA 1.080 0.000 NA 7.070

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
pararetrovirus PARA-RT pararetrovirus PARA-RT 5 0.00103
CRM Ty3-GAG CRM Ty3-GAG 50 0.01029
Reina Ty3-GAG Reina Ty3-GAG 1 0.00021
Tekay Ty3-GAG Tekay Ty3-GAG 602 0.12392
Tekay Ty3-INT Tekay Ty3-INT 1 0.00021
Chlamyvir Ty3-PROT Chlamyvir Ty3-PROT 25 0.00515
Reina Ty3-PROT Reina Ty3-PROT 32 0.00659
Tekay Ty3-PROT Tekay Ty3-PROT 254 0.05228
Athila Ty3-RH Athila Ty3-RH 1 0.00021
CRM Ty3-RT CRM Ty3-RT 50 0.01029
Chlamyvir Ty3-RT Chlamyvir Ty3-RT 24 0.00494
Galadriel Ty3-RT Galadriel Ty3-RT 3 0.00062
Reina Ty3-RT Reina Ty3-RT 97 0.01997
Tekay Ty3-RT Tekay Ty3-RT 979 0.20152
chromo-unclass Ty3-RT chromo-unclass Ty3-RT 2 0.00041

clusters with similarity:

Cluster Number of similarity hits
48 2000
70 1730
337 2

clusters connected through mates:

Cluster Number of shared
read pairs		 k
70 257 0.362
48 250 0.184
101 4 0.00462
2 3 0.00155
3 3 0.000936
14 3 0.00151
39 3 0.00223
12100 3 0.00774
16600 3 0.00774
6 2 0.00066
67 2 0.00161
84 2 0.00177
165 2 0.00388
4750 2 0.00517
12000 2 0.00516
14700 2 0.00516
20000 2 0.00516
30500 2 0.00517
35500 2 0.00517
37000 2 0.00517
59100 2 0.00517
10 1 0.000509
34 1 0.00064
41 1 0.00103
47 1 0.000748
49 1 0.000519
55 1 0.000907
56 1 0.000993
88 1 0.000963
94 1 0.00138
169 1 0.0018
185 1 0.00151
3750 1 0.00257
4800 1 0.00258
4930 1 0.00258
7190 1 0.00257
9560 1 0.00258
10500 1 0.00258
17200 1 0.00259
19300 1 0.00258
22000 1 0.00258
22000 1 0.00258
50800 1 0.00258
58200 1 0.00258
60800 1 0.00258
70300 1 0.00258

CL63 ----> CL70

image

No. of shared pairs: :257

CL63 ----> CL48

image

No. of shared pairs: :250