Cluster no. 142

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Cluster is part of supercluster: 10

Cluster characteristics:

size 2332
size_real 2332
ecount 70046
supercluster 10
annotations_summary 22.26% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RT
13.46% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-GAG
8.83% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-RH
7.20% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-PROT
1.29% Class_I/LTR/Ty3_gypsy/chromovirus/Chlamyvir:Ty3-RT
0.39% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RH
0.13% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH
0.09% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RT
0.09% Class_I/LTR/Ty3_gypsy/non-chromovirus/Selgy:Ty3-RH
0.04% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-GAG
0.04% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-unclass:Ty3-PROT
0.04% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-PROT
pair_completeness 0.721033210332103
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.000428816466552316
satellite_probability 1.17014641654426e-22
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S8 0
S5 821
S4 725
S7 0
S9 2
S6 779
S2 2
S1 3
S3 0
comparative analysis - number of edges between species:
S8 S5 S4 S7 S9 S6 S2 S1 S3
S8 0 0 0.0 0 0.0 0.0 0.0 0.0 0
S5 0 9260 7940.0 0 8.0 8210.0 13.0 14.0 0
S4 0 7940 6650.0 0 5.5 7100.0 14.0 13.0 0
S7 0 0 0.0 0 0.0 0.0 0.0 0.0 0
S9 0 8 5.5 0 0.0 6.5 0.0 0.0 0
S6 0 8210 7100.0 0 6.5 7450.0 11.5 11.5 0
S2 0 13 14.0 0 0.0 11.5 0.0 0.5 0
S1 0 14 13.0 0 0.0 11.5 0.5 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 NA NA NA NA NA NA NA NA NA
S5 NA 1.000 1.010 NA 1.100 0.992 0.918 0.988 NA
S4 NA 1.010 0.987 NA 0.887 1.000 1.160 1.070 NA
S7 NA NA NA NA NA NA NA NA NA
S9 NA 1.100 0.887 NA 0.000 0.999 0.000 0.000 NA
S6 NA 0.992 1.000 NA 0.999 1.010 0.906 0.906 NA
S2 NA 0.918 1.160 NA 0.000 0.906 0.000 23.000 NA
S1 NA 0.988 1.070 NA 0.000 0.906 23.000 0.000 NA
S3 NA NA NA NA NA NA NA NA NA

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
CRM Ty3-GAG CRM Ty3-GAG 1 0.00043
Tekay Ty3-GAG Tekay Ty3-GAG 314 0.13465
Reina Ty3-PROT Reina Ty3-PROT 1 0.00043
Tekay Ty3-PROT Tekay Ty3-PROT 168 0.07204
chromo-unclass Ty3-PROT chromo-unclass Ty3-PROT 1 0.00043
Reina Ty3-RH Reina Ty3-RH 3 0.00129
Selgy Ty3-RH Selgy Ty3-RH 2 0.00086
TatV Ty3-RH TatV Ty3-RH 9 0.00386
Tekay Ty3-RH Tekay Ty3-RH 206 0.08834
Chlamyvir Ty3-RT Chlamyvir Ty3-RT 30 0.01286
Reina Ty3-RT Reina Ty3-RT 2 0.00086
Tekay Ty3-RT Tekay Ty3-RT 519 0.22256

clusters with similarity:

Cluster Number of similarity hits
86 621
95 364
42 2
149 1

clusters connected through mates:

Cluster Number of shared
read pairs		 k
95 92 0.125
86 88 0.128
837 9 0.0447
1930 5 0.0259
1800 4 0.0205
4300 4 0.0209
6 3 0.00106
149 3 0.00974
10900 3 0.0157
12600 3 0.0157
2 2 0.00115
34 2 0.00146
84 2 0.00214
3710 2 0.0104
44700 2 0.0105
65300 2 0.0105
68300 2 0.0105
3 1 0.000332
10 1 0.000565
14 1 0.000557
20 1 0.000909
43 1 0.000691
45 1 0.000617
49 1 0.000578
55 1 0.0011
56 1 0.00123
62 1 0.00165
81 1 0.00179
87 1 0.00123
89 1 0.00151
117 1 0.00179
122 1 0.00261
134 1 0.00407
135 1 0.00243
138 1 0.00255
556 1 0.00503
8910 1 0.00526
10600 1 0.00524
19800 1 0.00528
22800 1 0.00526
70000 1 0.00526

CL142 ----> CL95

image

No. of shared pairs: :92

CL142 ----> CL86

image

No. of shared pairs: :88