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Solenopsis invicta (Red fire ant, M01_SB) vs Bombus impatiens (Common eastern bumblebee) LastZ results

Solenopsis invicta (Red fire ant, M01_SB) (Solenopsis invicta, UNIL_Sinv_3.0) and Bombus impatiens (Common eastern bumblebee) (Bombus impatiens, BIMP_2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 106. Solenopsis invicta (Red fire ant, M01_SB) 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

ParameterSolenopsis invicta (Red fire ant, M01_SB)Bombus impatiens (Common eastern bumblebee)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 153,071 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Solenopsis invicta (Red fire ant, M01_SB)

Uncovered: 322,783,135 out of 378,101,515
Covered: 55,318,380 out of 378,101,515

Uncovered: 6,645,268 out of 24,708,769
Matches: 12,622,893 out of 24,708,769
Mismatches: 5,061,806 out of 24,708,769
Insertions: 378,802 out of 24,708,769
Identity over aligned base-pairs: 69.9%

Bombus impatiens (Common eastern bumblebee)

Uncovered: 197,854,656 out of 246,856,484
Covered: 49,001,828 out of 246,856,484

Uncovered: 2,195,588 out of 18,806,354
Matches: 11,802,292 out of 18,806,354
Mismatches: 4,525,231 out of 18,806,354
Insertions: 283,243 out of 18,806,354
Identity over aligned base-pairs: 71.1%

Block size distribution

Size range All 153,071 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
577
3.8 kb
10 bp - 100 bp
16,886
1.1 Mb
3,889
271.3 kb
100 bp - 1 kb
124,153
41.6 Mb
24,519
8.4 Mb
1 kb - 10 kb
11,451
19.6 Mb
7,329
19.4 Mb
10 kb - 100 kb
4
50.1 kb
878
22.5 Mb
100 kb - 1 Mb
61
11.8 Mb