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Pythium irregulare vs Phytophthora parasitica LastZ results

Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_scaffolds_v1) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium irregulare 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

ParameterPythium irregularePhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 41,627 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium irregulare

Uncovered: 22,709,802 out of 42,968,084
Covered: 20,258,282 out of 42,968,084

Uncovered: 4,470,160 out of 20,543,058
Matches: 10,387,014 out of 20,543,058
Mismatches: 4,940,056 out of 20,543,058
Insertions: 745,828 out of 20,543,058
Identity over aligned base-pairs: 64.6%

Phytophthora parasitica

Uncovered: 32,785,481 out of 55,229,644
Covered: 22,444,163 out of 55,229,644

Uncovered: 8,878,588 out of 27,601,672
Matches: 12,217,743 out of 27,601,672
Mismatches: 5,969,028 out of 27,601,672
Insertions: 536,313 out of 27,601,672
Identity over aligned base-pairs: 65.3%

Block size distribution

Size range All 41,627 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
184
961.0 bp
10 bp - 100 bp
4,467
300.8 kb
1,016
71.5 kb
100 bp - 1 kb
28,764
11.8 Mb
9,750
4.4 Mb
1 kb - 10 kb
8,189
14.4 Mb
6,825
17.5 Mb
10 kb - 100 kb
23
297.9 kb
310
4.9 Mb