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Giardia lamblia vs Phytophthora kernoviae LastZ results

Giardia lamblia (Giardia lamblia, GL2) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,510 alignment blocks

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

Uncovered: 10,792,965 out of 11,192,215
Covered: 399,250 out of 11,192,215

Uncovered: 8,928,871 out of 9,322,001
Matches: 229,579 out of 9,322,001
Mismatches: 144,873 out of 9,322,001
Insertions: 18,678 out of 9,322,001
Identity over aligned base-pairs: 58.4%

Phytophthora kernoviae

Uncovered: 42,633,567 out of 43,208,681
Covered: 575,114 out of 43,208,681

Uncovered: 10,936,561 out of 11,344,308
Matches: 241,369 out of 11,344,308
Mismatches: 152,103 out of 11,344,308
Insertions: 14,275 out of 11,344,308
Identity over aligned base-pairs: 59.2%

Block size distribution

Size range All 1,510 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4
16.0 bp
10 bp - 100 bp
191
13.6 kb
67
5.1 kb
100 bp - 1 kb
1,169
436.9 kb
701
312.0 kb
1 kb - 10 kb
146
216.0 kb
187
349.5 kb