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Bombus terrestris (Buff-tailed bumblebee) vs Atta cephalotes (Leaf-cutter ant) LastZ results

Bombus terrestris (Buff-tailed bumblebee) (Bombus terrestris, Bter_1.0) and Atta cephalotes (Leaf-cutter ant) (Atta cephalotes, Attacep1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 91. Bombus terrestris (Buff-tailed bumblebee) was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterBombus terrestris (Buff-tailed bumblebee)Atta cephalotes (Leaf-cutter ant)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 150,438 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Bombus terrestris (Buff-tailed bumblebee)

Uncovered: 198,478,259 out of 248,654,244
Covered: 50,175,985 out of 248,654,244

Uncovered: 2,131,260 out of 18,548,448
Matches: 11,570,078 out of 18,548,448
Mismatches: 4,552,761 out of 18,548,448
Insertions: 294,349 out of 18,548,448
Identity over aligned base-pairs: 70.5%

Atta cephalotes (Leaf-cutter ant)

Uncovered: 257,563,860 out of 317,690,795
Covered: 60,126,935 out of 317,690,795

Uncovered: 1,824,938 out of 17,986,937
Matches: 11,426,178 out of 17,986,937
Mismatches: 4,421,879 out of 17,986,937
Insertions: 313,942 out of 17,986,937
Identity over aligned base-pairs: 70.7%

Block size distribution

Size range All 150,438 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
517
3.5 kb
10 bp - 100 bp
17,738
1.2 Mb
6,355
439.5 kb
100 bp - 1 kb
119,552
39.9 Mb
32,150
11.3 Mb
1 kb - 10 kb
12,460
23.2 Mb
7,640
20.2 Mb
10 kb - 100 kb
171
4.2 Mb
981
25.4 Mb
100 kb - 1 Mb
60
11.1 Mb