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Bombus terrestris (Buff-tailed bumblebee) vs Solenopsis invicta (Red fire ant, M01_SB) LastZ results

Bombus terrestris (Buff-tailed bumblebee) (Bombus terrestris, Bter_1.0) 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. 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)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 153,684 alignment blocks

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

Uncovered: 198,595,959 out of 248,654,244
Covered: 50,058,285 out of 248,654,244

Uncovered: 2,031,516 out of 18,548,448
Matches: 11,738,823 out of 18,548,448
Mismatches: 4,498,696 out of 18,548,448
Insertions: 279,413 out of 18,548,448
Identity over aligned base-pairs: 71.1%

Solenopsis invicta (Red fire ant, M01_SB)

Uncovered: 321,358,376 out of 378,101,515
Covered: 56,743,139 out of 378,101,515

Uncovered: 6,583,580 out of 24,708,769
Matches: 12,629,644 out of 24,708,769
Mismatches: 5,113,126 out of 24,708,769
Insertions: 382,419 out of 24,708,769
Identity over aligned base-pairs: 69.7%

Block size distribution

Size range All 153,684 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
595
4.0 kb
10 bp - 100 bp
16,831
1.1 Mb
3,931
276.5 kb
100 bp - 1 kb
124,340
41.3 Mb
25,738
8.7 Mb
1 kb - 10 kb
11,895
21.6 Mb
7,356
20.7 Mb
10 kb - 100 kb
23
607.1 kb
849
21.3 Mb
100 kb - 1 Mb
67
13.8 Mb