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Atta cephalotes (Leaf-cutter ant) vs Nasonia vitripennis (Jewel wasp, AsymCx) LastZ results

Atta cephalotes (Leaf-cutter ant) (Atta cephalotes, Attacep1.0) and Nasonia vitripennis (Jewel wasp, AsymCx) (Nasonia vitripennis, Nvit_psr_1.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 102. 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)Nasonia vitripennis (Jewel wasp, AsymCx)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 78,838 alignment blocks

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

Uncovered: 292,909,184 out of 317,690,795
Covered: 24,781,611 out of 317,690,795

Uncovered: 4,664,718 out of 17,986,937
Matches: 9,026,049 out of 17,986,937
Mismatches: 4,016,116 out of 17,986,937
Insertions: 280,054 out of 17,986,937
Identity over aligned base-pairs: 67.8%

Nasonia vitripennis (Jewel wasp, AsymCx)

Uncovered: 272,560,639 out of 297,309,692
Covered: 24,749,053 out of 297,309,692

Uncovered: 8,434,770 out of 22,806,936
Matches: 9,595,972 out of 22,806,936
Mismatches: 4,400,633 out of 22,806,936
Insertions: 375,561 out of 22,806,936
Identity over aligned base-pairs: 66.8%

Block size distribution

Size range All 78,838 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
356
2.3 kb
10 bp - 100 bp
12,234
791.2 kb
4,125
275.4 kb
100 bp - 1 kb
60,012
19.6 Mb
19,115
6.6 Mb
1 kb - 10 kb
6,223
10.4 Mb
7,643
19.6 Mb
10 kb - 100 kb
13
154.9 kb
281
4.5 Mb