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Apis mellifera (DH4) vs Solenopsis invicta LastZ results

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

Statistics over 124,547 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Apis mellifera (DH4)

Uncovered: 180,372,506 out of 225,250,884
Covered: 44,878,378 out of 225,250,884

Uncovered: 1,955,930 out of 18,346,913
Matches: 11,565,551 out of 18,346,913
Mismatches: 4,532,021 out of 18,346,913
Insertions: 293,411 out of 18,346,913
Identity over aligned base-pairs: 70.6%

Solenopsis invicta

Uncovered: 350,911,381 out of 398,994,629
Covered: 48,083,248 out of 398,994,629

Uncovered: 5,520,809 out of 22,635,573
Matches: 12,076,795 out of 22,635,573
Mismatches: 4,668,400 out of 22,635,573
Insertions: 369,569 out of 22,635,573
Identity over aligned base-pairs: 70.6%

Block size distribution

Size range All 124,547 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
488
3.3 kb
10 bp - 100 bp
13,863
889.2 kb
2,176
154.5 kb
100 bp - 1 kb
99,824
33.7 Mb
16,331
5.7 Mb
1 kb - 10 kb
10,361
18.4 Mb
4,976
15.1 Mb
10 kb - 100 kb
11
129.5 kb
948
23.9 Mb
100 kb - 1 Mb
45
8.3 Mb