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Atta cephalotes (Leaf-cutter ant) vs Bombus impatiens (Common eastern bumblebee) LastZ results

Atta cephalotes (Leaf-cutter ant) (Atta cephalotes, Attacep1.0) and Bombus impatiens (Common eastern bumblebee) (Bombus impatiens, BIMP_2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 106. Atta cephalotes (Leaf-cutter ant) 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

ParameterAtta cephalotes (Leaf-cutter ant)Bombus impatiens (Common eastern bumblebee)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 160,431 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Atta cephalotes (Leaf-cutter ant)

Uncovered: 255,546,912 out of 317,690,795
Covered: 62,143,883 out of 317,690,795

Uncovered: 1,853,718 out of 17,986,937
Matches: 11,438,685 out of 17,986,937
Mismatches: 4,383,322 out of 17,986,937
Insertions: 311,212 out of 17,986,937
Identity over aligned base-pairs: 70.9%

Bombus impatiens (Common eastern bumblebee)

Uncovered: 197,500,231 out of 246,856,484
Covered: 49,356,253 out of 246,856,484

Uncovered: 2,304,062 out of 18,806,354
Matches: 11,607,383 out of 18,806,354
Mismatches: 4,597,267 out of 18,806,354
Insertions: 297,642 out of 18,806,354
Identity over aligned base-pairs: 70.3%

Block size distribution

Size range All 160,431 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
604
3.9 kb
10 bp - 100 bp
19,233
1.2 Mb
7,518
510.3 kb
100 bp - 1 kb
125,849
42.4 Mb
34,458
11.9 Mb
1 kb - 10 kb
14,722
26.1 Mb
10,789
25.9 Mb
10 kb - 100 kb
23
275.1 kb
910
22.3 Mb
100 kb - 1 Mb
54
9.5 Mb