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Atta cephalotes (Leaf-cutter ant) vs Solenopsis invicta (Red fire ant, M01_SB) LastZ results

Atta cephalotes (Leaf-cutter ant) (Atta cephalotes, Attacep1.0) and Solenopsis invicta (Red fire ant, M01_SB) (Solenopsis invicta, UNIL_Sinv_3.0) 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)Solenopsis invicta (Red fire ant, M01_SB)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 593,258 alignment blocks

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

Uncovered: 74,955,354 out of 317,690,795
Covered: 242,735,441 out of 317,690,795

Uncovered: 157,666 out of 17,986,937
Matches: 15,091,803 out of 17,986,937
Mismatches: 2,587,397 out of 17,986,937
Insertions: 150,071 out of 17,986,937
Identity over aligned base-pairs: 84.6%

Solenopsis invicta (Red fire ant, M01_SB)

Uncovered: 116,878,695 out of 378,101,515
Covered: 261,222,820 out of 378,101,515

Uncovered: 2,091,435 out of 24,708,769
Matches: 17,807,524 out of 24,708,769
Mismatches: 4,443,388 out of 24,708,769
Insertions: 366,422 out of 24,708,769
Identity over aligned base-pairs: 78.7%

Block size distribution

Size range All 593,258 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7,004
43.2 kb
10 bp - 100 bp
109,935
6.8 Mb
64,907
4.4 Mb
100 bp - 1 kb
380,597
136.3 Mb
217,353
71.0 Mb
1 kb - 10 kb
95,427
195.6 Mb
36,352
81.8 Mb
10 kb - 100 kb
293
3.6 Mb
798
16.0 Mb
100 kb - 1 Mb
2
266.2 kb
140
56.0 Mb
1 Mb - 10 Mb
54
113.5 Mb