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Giardia lamblia vs Pythium irregulare LastZ results

Giardia lamblia (Giardia lamblia, GL2) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Giardia lamblia 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

ParameterGiardia lambliaPythium irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,676 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Giardia lamblia

Uncovered: 10,792,765 out of 11,192,215
Covered: 399,450 out of 11,192,215

Uncovered: 8,930,230 out of 9,322,001
Matches: 228,563 out of 9,322,001
Mismatches: 143,780 out of 9,322,001
Insertions: 19,428 out of 9,322,001
Identity over aligned base-pairs: 58.3%

Pythium irregulare

Uncovered: 42,364,391 out of 42,968,084
Covered: 603,693 out of 42,968,084

Uncovered: 20,000,467 out of 20,543,058
Matches: 320,709 out of 20,543,058
Mismatches: 200,559 out of 20,543,058
Insertions: 21,323 out of 20,543,058
Identity over aligned base-pairs: 59.1%

Block size distribution

Size range All 1,676 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5
21.0 bp
10 bp - 100 bp
230
16.0 kb
90
6.4 kb
100 bp - 1 kb
1,296
475.8 kb
748
328.3 kb
1 kb - 10 kb
145
224.8 kb
193
381.8 kb