Cluster no. 20

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Cluster is part of supercluster: 14

Cluster characteristics:

size 6937
size_real 6937
ecount 89714
supercluster 14
annotations_summary 21.71% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-INT
12.37% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RT
10.28% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-RH
10.18% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-GAG
5.68% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-PROT
0.14% organelle/mitochondria
0.09% Class_I/LTR/Ty3_gypsy/chromovirus/Reina:Ty3-RH
0.09% Class_I/LTR/Ty3_gypsy/chromovirus/CRM:Ty3-CHDCR
0.03% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-RH
0.03% Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV:Ty3-RH
0.03% Class_I/LTR/Ty3_gypsy/chromovirus/Tekay:Ty3-INT
0.01% Class_I/LTR/Ty3_gypsy/chromovirus/Tcn1:Ty3-INT
0.01% Class_I/LTR/Ty3_gypsy/chromovirus/chromo-unclass:Ty3-INT
0.01% Class_I/LTR/Ty1_copia/Ivana:Ty1-INT
0.01% Class_I/LTR/Ty1_copia/SIRE:Ty1-RT
pair_completeness 0.853326208923324
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.000576618134640334
satellite_probability 9.43324980190488e-24
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S2 2240
S1 2360
S3 2340
comparative analysis - number of edges between species:
S2 S1 S3
S2 8930 9890 9400
S1 9890 11100 10600
S3 9400 10600 9960
comparative analysis - observed/expected number of edges between species
S2 S1 S3
S2 1.010 0.997 0.998
S1 0.997 0.998 1.010
S3 0.998 1.010 0.996

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
mitochondria mitochondria 10 0.00144
Ivana Ty1-INT Ivana Ty1-INT 1 0.00014
SIRE Ty1-RT SIRE Ty1-RT 1 0.00014
CRM Ty3-CHDCR CRM Ty3-CHDCR 6 0.00086
CRM Ty3-GAG CRM Ty3-GAG 706 0.10177
CRM Ty3-INT CRM Ty3-INT 1506 0.21710
Tcn1 Ty3-INT Tcn1 Ty3-INT 1 0.00014
Tekay Ty3-INT Tekay Ty3-INT 2 0.00029
chromo-unclass Ty3-INT chromo-unclass Ty3-INT 1 0.00014
CRM Ty3-PROT CRM Ty3-PROT 394 0.05680
CRM Ty3-RH CRM Ty3-RH 713 0.10278
Reina Ty3-RH Reina Ty3-RH 6 0.00086
TatV Ty3-RH TatV Ty3-RH 2 0.00029
Tcn1 Ty3-RH Tcn1 Ty3-RH 2 0.00029
CRM Ty3-RT CRM Ty3-RT 858 0.12368

clusters with similarity:

Cluster Number of similarity hits
96 4
30 1

clusters connected through mates:

Cluster Number of shared
read pairs		 k
96 73 0.128
4 5 0.00197
9 4 0.00267
5830 4 0.0145
13 3 0.00178
34 3 0.00546
1680 3 0.0108
4260 3 0.0109
6620 3 0.0108
9550 3 0.0109
12700 3 0.0109
6 2 0.00117
8 2 0.00236
21 2 0.00187
25 2 0.00175
27 2 0.00136
697 2 0.00703
2620 2 0.00719
2780 2 0.00719
4680 2 0.00722
5400 2 0.00723
5580 2 0.00723
6830 2 0.00726
7030 2 0.00723
7340 2 0.00723
7460 2 0.00723
13700 2 0.00725
29900 2 0.00726
38600 2 0.00726
38800 2 0.00726
39600 2 0.00726
43800 2 0.00726
45100 2 0.00726
48200 2 0.00726
49300 2 0.00726
51000 2 0.00726
1 1 0.00044
11 1 0.000663
15 1 0.00168
22 1 8e-04
24 1 0.000725
26 1 0.000693
28 1 0.000649
30 1 0.000737
32 1 0.00071
37 1 0.000718
40 1 0.00112
41 1 0.00225
43 1 0.00154
45 1 0.00141
46 1 0.00117
48 1 0.00127
49 1 0.00118
50 1 0.00115
59 1 0.00145
60 1 0.00145
61 1 0.00233
64 1 0.00172
68 1 0.00111
71 1 0.00186
77 1 0.00229
90 1 0.00148
91 1 0.00249
106 1 0.00241
207 1 0.00327
379 1 0.00351
473 1 0.00344
1470 1 0.00358
1740 1 0.0036
2510 1 0.00361
2630 1 0.0036
3160 1 0.00363
3270 1 0.0036
3470 1 0.0036
3980 1 0.00362
4050 1 0.00361
4670 1 0.00362
5370 1 0.00362
6030 1 0.00362
6680 1 0.00363
6800 1 0.00362
7500 1 0.00363
7670 1 0.00363
8100 1 0.00362
8650 1 0.00364
8650 1 0.00362
8660 1 0.00364
8750 1 0.00362
8840 1 0.00362
9870 1 0.00362
10500 1 0.00362
10900 1 0.00362
11000 1 0.00364
12300 1 0.00362
12400 1 0.00362
14100 1 0.00362
14900 1 0.00363
15000 1 0.00363
16500 1 0.00363
18000 1 0.00363
18500 1 0.00363
20800 1 0.00363
21600 1 0.00363
23800 1 0.00363
24000 1 0.00363
24600 1 0.00363
25200 1 0.00363
29900 1 0.00363
31300 1 0.00363
34400 1 0.00363
34600 1 0.00363
34900 1 0.00363
35300 1 0.00363
38600 1 0.00363
39900 1 0.00363
41600 1 0.00363
41900 1 0.00363
42600 1 0.00363
44300 1 0.00363
44300 1 0.00363
47300 1 0.00363
47500 1 0.00363
48100 1 0.00363
48200 1 0.00363
48700 1 0.00363
49700 1 0.00363
50200 1 0.00363
51600 1 0.00363
51600 1 0.00363

CL20 ----> CL96

image

No. of shared pairs: :73