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Apis mellifera (Honey bee, DH4) vs Solenopsis invicta (Red fire ant, M01_SB) LastZ results

Apis mellifera (Honey bee, DH4) (Apis mellifera, Amel_HAv3.1) 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. Apis mellifera (Honey bee, DH4) 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

ParameterApis mellifera (Honey bee, DH4)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 126,352 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Apis mellifera (Honey bee, DH4)

Uncovered: 180,092,905 out of 225,250,884
Covered: 45,157,979 out of 225,250,884

Uncovered: 1,957,089 out of 18,346,913
Matches: 11,660,695 out of 18,346,913
Mismatches: 4,432,014 out of 18,346,913
Insertions: 297,115 out of 18,346,913
Identity over aligned base-pairs: 71.1%

Solenopsis invicta (Red fire ant, M01_SB)

Uncovered: 329,432,971 out of 378,101,515
Covered: 48,668,544 out of 378,101,515

Uncovered: 7,187,442 out of 24,708,769
Matches: 12,343,644 out of 24,708,769
Mismatches: 4,789,699 out of 24,708,769
Insertions: 387,984 out of 24,708,769
Identity over aligned base-pairs: 70.4%

Block size distribution

Size range All 126,352 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
505
3.5 kb
10 bp - 100 bp
14,267
911.4 kb
2,386
166.6 kb
100 bp - 1 kb
100,705
34.1 Mb
15,855
5.5 Mb
1 kb - 10 kb
10,871
19.1 Mb
5,267
15.7 Mb
10 kb - 100 kb
4
44.4 kb
906
22.4 Mb
100 kb - 1 Mb
54
10.4 Mb