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Albugo laibachii vs Giardia lamblia LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Giardia lamblia (Giardia lamblia, GL2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Albugo laibachii 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

ParameterAlbugo laibachiiGiardia lamblia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,156 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Albugo laibachii

Uncovered: 32,316,126 out of 32,766,811
Covered: 450,685 out of 32,766,811

Uncovered: 15,476,690 out of 15,902,867
Matches: 245,934 out of 15,902,867
Mismatches: 163,816 out of 15,902,867
Insertions: 16,427 out of 15,902,867
Identity over aligned base-pairs: 57.7%

Giardia lamblia

Uncovered: 10,862,572 out of 11,192,215
Covered: 329,643 out of 11,192,215

Uncovered: 8,999,141 out of 9,322,001
Matches: 185,111 out of 9,322,001
Mismatches: 121,913 out of 9,322,001
Insertions: 15,836 out of 9,322,001
Identity over aligned base-pairs: 57.3%

Block size distribution

Size range All 1,156 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
4.0 bp
10 bp - 100 bp
159
11.8 kb
95
7.1 kb
100 bp - 1 kb
877
342.4 kb
522
242.1 kb
1 kb - 10 kb
119
174.0 kb
147
279.1 kb