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Giardia lamblia vs Phytophthora lateralis LastZ results

Giardia lamblia (Giardia lamblia, GL2) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 lambliaPhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,373 alignment blocks

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

Uncovered: 10,829,494 out of 11,192,215
Covered: 362,721 out of 11,192,215

Uncovered: 8,967,504 out of 9,322,001
Matches: 205,982 out of 9,322,001
Mismatches: 131,208 out of 9,322,001
Insertions: 17,307 out of 9,322,001
Identity over aligned base-pairs: 58.1%

Phytophthora lateralis

Uncovered: 43,505,609 out of 43,981,379
Covered: 475,770 out of 43,981,379

Uncovered: 13,835,437 out of 14,242,768
Matches: 238,749 out of 14,242,768
Mismatches: 152,853 out of 14,242,768
Insertions: 15,729 out of 14,242,768
Identity over aligned base-pairs: 58.6%

Block size distribution

Size range All 1,373 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9
49.0 bp
10 bp - 100 bp
167
11.9 kb
78
5.8 kb
100 bp - 1 kb
1,084
399.1 kb
648
281.9 kb
1 kb - 10 kb
113
168.8 kb
139
292.3 kb