Atta cephalotes vs Apis mellifera (DH4) LastZ results

Atta cephalotes (Atta cephalotes, Attacep1.0) and Apis mellifera (DH4) (Apis mellifera, Amel_HAv3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 102. Atta cephalotes 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 cephalotesApis mellifera (DH4)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 116,638 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Atta cephalotes

Uncovered: 268,282,592 out of 317,690,795
Covered: 49,408,203 out of 317,690,795

Uncovered: 1,928,515 out of 17,986,937
Matches: 11,447,180 out of 17,986,937
Mismatches: 4,267,475 out of 17,986,937
Insertions: 343,767 out of 17,986,937
Identity over aligned base-pairs: 71.3%

Apis mellifera (DH4)

Uncovered: 177,583,844 out of 225,250,884
Covered: 47,667,040 out of 225,250,884

Uncovered: 2,010,105 out of 18,346,913
Matches: 11,485,172 out of 18,346,913
Mismatches: 4,538,954 out of 18,346,913
Insertions: 312,682 out of 18,346,913
Identity over aligned base-pairs: 70.3%

Block size distribution

Size range All 116,638 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
497
3.4 kb
10 bp - 100 bp
12,756
807.7 kb
2,406
166.8 kb
100 bp - 1 kb
90,644
31.2 Mb
16,012
5.6 Mb
1 kb - 10 kb
12,717
24.3 Mb
6,288
18.7 Mb
10 kb - 100 kb
24
293.8 kb
1,001
23.5 Mb
100 kb - 1 Mb
48
8.6 Mb