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Pythium irregulare vs Phytophthora lateralis LastZ results

Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_scaffolds_v1) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 37,718 alignment blocks

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

Uncovered: 25,080,957 out of 42,968,084
Covered: 17,887,127 out of 42,968,084

Uncovered: 6,434,096 out of 20,543,058
Matches: 9,179,975 out of 20,543,058
Mismatches: 4,276,102 out of 20,543,058
Insertions: 652,885 out of 20,543,058
Identity over aligned base-pairs: 65.1%

Phytophthora lateralis

Uncovered: 25,444,992 out of 43,981,379
Covered: 18,536,387 out of 43,981,379

Uncovered: 3,206,692 out of 14,242,768
Matches: 7,437,153 out of 14,242,768
Mismatches: 3,281,421 out of 14,242,768
Insertions: 317,502 out of 14,242,768
Identity over aligned base-pairs: 67.4%

Block size distribution

Size range All 37,718 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
161
837.0 bp
10 bp - 100 bp
4,151
278.5 kb
1,130
80.5 kb
100 bp - 1 kb
26,725
10.8 Mb
10,158
4.4 Mb
1 kb - 10 kb
6,662
11.8 Mb
5,743
14.6 Mb
10 kb - 100 kb
19
238.8 kb
255
4.0 Mb