Cluster no. 115

Go back to cluster table

Cluster is part of supercluster: 59

Cluster characteristics:

size 667
size_real 667
ecount 3584
supercluster 59
annotations_summary 17.84% Class_I/LTR/Ty1_copia/TAR:Ty1-RT
14.09% Class_I/LTR/Ty1_copia/TAR:Ty1-INT
8.25% Class_I/LTR/Ty1_copia/TAR:Ty1-RH
3.45% Class_I/LTR/Ty1_copia/TAR:Ty1-PROT
3.30% Class_I/LTR/Ty1_copia/TAR:Ty1-GAG
0.45% Class_I/LTR/Ty1_copia/Ikeros:Ty1-INT
0.30% Class_I/LTR/Ty1_copia/Ivana:Ty1-INT
0.15% organelle/mitochondria
0.15% Class_I/LTR/Ty3_gypsy/non-chromovirus/nonchromo-outgroup:Ty3-INT
0.15% Class_I/LTR/Ty1_copia/Ivana:Ty1-RH
pair_completeness 0.755263157894737
pbs_score None
TR_score None
TR_monomer_length None
loop_index 0.00149925037481259
satellite_probability 5.68788576307886e-23
consensus None
TAREAN_annotation Other
orientation_score 1

comparative analysis:


Comparative analysis - species read counts:
Species Read count
S2 204
S1 239
S3 224
comparative analysis - number of edges between species:
S2 S1 S3
S2 379 395 382
S1 395 462 382
S3 382 382 425
comparative analysis - observed/expected number of edges between species
S2 S1 S3
S2 1.020 0.988 0.996
S1 0.988 1.080 0.929
S3 0.996 0.929 1.080

protein domains:

protein domains:


Reads annotation summary

  cl_string domain Freq proportion
mitochondria mitochondria 1 0.0015
TAR Ty1-GAG TAR Ty1-GAG 22 0.0330
Ikeros Ty1-INT Ikeros Ty1-INT 3 0.0045
Ivana Ty1-INT Ivana Ty1-INT 2 0.0030
TAR Ty1-INT TAR Ty1-INT 94 0.1409
TAR Ty1-PROT TAR Ty1-PROT 23 0.0345
Ivana Ty1-RH Ivana Ty1-RH 1 0.0015
TAR Ty1-RH TAR Ty1-RH 55 0.0825
TAR Ty1-RT TAR Ty1-RT 119 0.1784
nonchromo-outgroup Ty3-INT nonchromo-outgroup Ty3-INT 1 0.0015

clusters connected through mates:

Cluster Number of shared
read pairs		 k
664 3 0.0556
11 2 0.00156
80 2 0.00253
2600 2 0.0417
7940 2 0.0417
8500 2 0.0417
11100 2 0.0417
26000 2 0.0421
31300 2 0.0421
8 1 0.00162
12 1 0.000572
38 1 0.00102
42 1 0.000942
48 1 0.00179
50 1 0.00156
67 1 0.00239
1140 1 0.0189
9580 1 0.0208
9630 1 0.0213
9730 1 0.0208
11100 1 0.0208
13200 1 0.0213
23200 1 0.0211
25200 1 0.0211
38700 1 0.0211
38700 1 0.0211
43900 1 0.0211
47400 1 0.0211