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Phaeodactylum tricornutum vs Pythium irregulare LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phaeodactylum tricornutum 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

ParameterPhaeodactylum tricornutumPythium irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,655 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phaeodactylum tricornutum

Uncovered: 25,695,917 out of 27,568,093
Covered: 1,872,176 out of 27,568,093

Uncovered: 16,057,245 out of 17,873,974
Matches: 1,090,875 out of 17,873,974
Mismatches: 647,566 out of 17,873,974
Insertions: 78,288 out of 17,873,974
Identity over aligned base-pairs: 60.0%

Pythium irregulare

Uncovered: 40,951,128 out of 42,968,084
Covered: 2,016,956 out of 42,968,084

Uncovered: 18,680,163 out of 20,543,058
Matches: 1,126,549 out of 20,543,058
Mismatches: 668,166 out of 20,543,058
Insertions: 68,180 out of 20,543,058
Identity over aligned base-pairs: 60.5%

Block size distribution

Size range All 5,655 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
11
56.0 bp
10 bp - 100 bp
847
59.9 kb
218
15.5 kb
100 bp - 1 kb
4,253
1.5 Mb
2,025
942.0 kb
1 kb - 10 kb
544
813.5 kb
870
1.4 Mb
10 kb - 100 kb
1
10.6 kb